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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/seqkit">Debian Med / seqkit</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326">eb1d2ff1</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-09-26T23:37:35+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.1+ds</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#7cdca301cbb4c2d5233c0eed1f6571d394148920">
doc/docs/download.md
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</li>
<li class="file-stats">
<a href="#25d4d7cf2f9cbc5b638136ee9d4049b6096fcba9">
doc/docs/usage.md
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<li class="file-stats">
<a href="#c47645c391ad0571c40779079363c9d48412e18b">
go.mod
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<li class="file-stats">
<a href="#5aa1ac64de2b0c4821af9393b44965020e4a521d">
go.sum
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<li class="file-stats">
<a href="#a02b528e8138ab6ad3eae788206eb69181c130ba">
seqkit/cmd/grep.go
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<li class="file-stats">
<a href="#32f77b9b26ba8c525e818703d5ae667b751cebef">
seqkit/cmd/replace.go
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<li class="file-stats">
<a href="#a081fd2a9409882bfb5fbf48cc5469d880b5a3a1">
seqkit/cmd/subseq.go
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<li class="file-stats">
<a href="#48404aa0fac3725b4a485b95bf89f1b19e6da31a">
seqkit/main.go
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<h4>Changes:</h4>
<li id="7cdca301cbb4c2d5233c0eed1f6571d394148920">
<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#7cdca301cbb4c2d5233c0eed1f6571d394148920"><strong>doc/docs/download.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,21 +3,19 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">SeqKit is implemented in <span class="p">[</span><span class="nv" style="color: #008080;">Go</span><span class="p">](</span><span class="sx" style="color: #d14;">https://golang.org/</span><span class="p">)</span> programming language,</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown">statically-linked executable binary files are <span class="p">[</span><span class="nv" style="color: #008080;">freely available</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown">Please cite:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="gt" style="color: #a00;">> **W Shen**, S Le, Y Li\*, F Hu\*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="gt" style="color: #a00;">> ***PLOS ONE***. [doi:10.1371/journal.pone.0163962](https://doi.org/10.1371/journal.pone.0163962).</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown">Please cite: <span class="gs" style="font-weight: 600;">**W Shen**</span>, S Le, Y Li<span class="se" style="color: #d14;">\*</span>, F Hu<span class="se" style="color: #d14;">\*</span>. SeqKit: 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="markdown"><span class="gs" style="font-weight: 600;">***PLOS ONE**</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>. <span class="p">[</span><span class="nv" style="color: #008080;">doi:10.1371/journal.pone.0163962</span><span class="p">](</span><span class="sx" style="color: #d14;">https://doi.org/10.1371/journal.pone.0163962</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown">OS |Arch |File, 中国镜像 |Download Count</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown">Linux |32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_linux_386.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">0.16.1</span>/seqkit_linux_386.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">0.16.1</span>/seqkit_linux_386.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">0.16.1</span>/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">0.16.1</span>/seqkit_linux_amd64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">0.16.1</span>/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">0.16.1</span>/seqkit_linux_arm64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">0.16.1</span>/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">0.16.1</span>/seqkit_darwin_amd64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">0.16.1</span>/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">0.16.1</span>/seqkit_darwin_arm64.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown">Windows|32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_windows_386.exe.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">0.16.1</span>/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">0.16.1</span>/seqkit_windows_386.exe.tar.gz)</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">Windows|<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_windows_amd64.exe.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">0.16.1</span>/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>|<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">0.16.1</span>/seqkit_windows_amd64.exe.tar.gz)</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">Linux |32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_linux_386.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">2.0.0</span>/seqkit_linux_386.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">2.0.0</span>/seqkit_linux_386.tar.gz)</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">2.0.0</span>/seqkit_linux_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">2.0.0</span>/seqkit_linux_amd64.tar.gz)</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">Linux |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_linux_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">2.0.0</span>/seqkit_linux_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">2.0.0</span>/seqkit_linux_arm64.tar.gz)</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_amd64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">2.0.0</span>/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">2.0.0</span>/seqkit_darwin_amd64.tar.gz)</span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">macOS |<span class="gs" style="font-weight: 600;">**arm64**</span> |<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_darwin_arm64.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">2.0.0</span>/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">2.0.0</span>/seqkit_darwin_arm64.tar.gz)</span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">Windows|32-bit |<span class="p">[</span><span class="nv" style="color: #008080;">seqkit_windows_386.exe.tar.gz</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">2.0.0</span>/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz</span><span class="p">)</span> |<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">2.0.0</span>/seqkit_windows_386.exe.tar.gz)</span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">Windows|<span class="gs" style="font-weight: 600;">**64-bit**</span>|<span class="p">[</span><span class="nv" style="color: #008080;">**seqkit_windows_amd64.exe.tar.gz**</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff left">2.0.0</span>/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>, <span class="nt" style="color: #000080;"><br/></span> <span class="p">[</span><span class="nv" style="color: #008080;">中国镜像</span><span class="p">](</span><span class="sx" style="color: #d14;">http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz</span><span class="p">)</span>|<span class="p">[</span><span class="nv" style="color: #008080;">![Github Releases (by Asset)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600</span><span class="p">)</span>](https://github.com/shenwei356/seqkit/releases/download/v<span class="idiff right">2.0.0</span>/seqkit_windows_amd64.exe.tar.gz)</span>
</pre>
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21
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
</pre>
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22
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Notes*</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,13 +47,13 @@ And then:</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="sb" style="color: #d14;"> conda install -c bioconda seqkit</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Method 3: Install via homebrew (latest stable version)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Method 3: Install via <span class="idiff left">[</span>homebrew<span class="idiff right">](https://brew.sh/)</span> (latest stable version)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install <span class="idiff left right">brewsci/bio/</span>seqkit</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install seqkit</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Method 4: For Go developer (latest stable/dev version)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="sb" style="color: #d14;"> go get -u github.com/shenwei356/seqkit/seqkit</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="sb" style="color: #d14;"> go get -u github.com/shenwei356/seqkit/<span class="idiff left">v2/</span>seqkit<span class="idiff right">/</span></span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Method 5: Docker based installation (latest stable/dev version)</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#25d4d7cf2f9cbc5b638136ee9d4049b6096fcba9"><strong>doc/docs/usage.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -425,7 +425,13 @@ Usage</td>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="markdown"><span class="p">```</span><span class="nl"> text</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="markdown">get subsequences by region/gtf/bed, including flanking sequences.</span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="markdown">Recommendation: use plain FASTA file, so seqkit could utilize FASTA index.</span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="markdown">Attentions:</span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="markdown"> 1. Use "seqkit grep" for extract subsets of sequences.</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="markdown"> "seqtk subseq seqs.fasta id.txt" equals to</span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="markdown"> "seqkit grep -f id.txt seqs.fasta"</span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="markdown">Recommendation:</span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="markdown"> 1. use plain FASTA file, so seqkit could utilize FASTA index.</span>
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="markdown">The definition of region is 1-based and with some custom design.</span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1407,6 +1413,8 @@ Attentions:</td>
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="markdown"> file, not the order of the query patterns. </span>
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="markdown"> But for FASTA file, you can use:</span>
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="markdown"> seqkit faidx seqs.fasta --infile-list IDs.txt</span>
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="markdown"> 6. For multiple patterns, you can either set "-p" multiple times, i.e.,</span>
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="markdown"> -p pattern1 -p pattern2, or give a file of patterns via "-f/--pattern-file".</span>
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="markdown">You can specify the sequence region for searching with the flag -R (--region).</span>
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="markdown">The definition of region is 1-based and with some custom design.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2539,6 +2547,13 @@ Special replacement symbols (only for replacing name not sequence):</td>
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2539
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2547
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<pre style="margin: 0;"> <span id="LC2547" class="line" lang="markdown"> {nr} Record number, starting from 1</span>
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<pre style="margin: 0;"> <span id="LC2548" class="line" lang="markdown"> {kv} Corresponding value of the key (captured variable $n) by key-value file,</span>
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2541
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<pre style="margin: 0;"> <span id="LC2549" class="line" lang="markdown"> n can be specified by flag -I (--key-capt-idx) (default: 1)</span>
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<pre style="margin: 0;">+<span id="LC2550" class="line" lang="markdown"> </span>
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2551
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<pre style="margin: 0;">+<span id="LC2551" class="line" lang="markdown">Special cases:</span>
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<pre style="margin: 0;">+<span id="LC2552" class="line" lang="markdown"> 1. If replacements contain '$', </span>
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<pre style="margin: 0;">+<span id="LC2553" class="line" lang="markdown"> a). If using '{kv}', you need use '$$$$' instead of a single '$':</span>
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<pre style="margin: 0;">+<span id="LC2554" class="line" lang="markdown"> -r '{kv}' -k <(sed 's/\$/$$$$/' kv.txt)</span>
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<pre style="margin: 0;">+<span id="LC2555" class="line" lang="markdown"> b). If not, use '$$':</span>
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<pre style="margin: 0;">+<span id="LC2556" class="line" lang="markdown"> -r 'xxx$$xx'</span>
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<pre style="margin: 0;"> <span id="LC2557" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC2558" class="line" lang="markdown">Usage:</span>
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<pre style="margin: 0;"> <span id="LC2559" class="line" lang="markdown"> seqkit replace [flags]</span>
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<li id="c47645c391ad0571c40779079363c9d48412e18b">
<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#c47645c391ad0571c40779079363c9d48412e18b"><strong>go.mod</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">module <a href="https://pkg.go.dev/github.com/shenwei356/seqkit" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/seqkit</a></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">module <a href="https://pkg.go.dev/github.com/shenwei356/seqkit/v2" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/seqkit<span class="idiff left right">/v2</span></a></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">go 1.17</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,12 +17,11 @@ require (</td>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/mattn/go-isatty@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-isatty</a> v0.0.13</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/mitchellh/go-homedir@v1.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/mitchellh/go-homedir</a> v1.1.0</span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/pkg/errors@v0.9.1" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/errors</a> v0.9.1</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/pkg/profile@v1.6.0" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/profile</a> v1.6.0</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.0</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.0</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.1</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bwt</a> v0.5.1</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/go-logging@v0.0.0-20171012171522-c6b9702d88ba" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/go-logging</a> v0.0.0-20171012171522-c6b9702d88ba</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/util@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.3.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.3.<span class="idiff left right">2</span></span>
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/xopen</a> v0.1.0</span>
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27
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/smallfish/simpleyaml@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/smallfish/simpleyaml</a> v0.1.0</span>
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28
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/spf13/cobra@v1.2.1" rel="nofollow noreferrer noopener" target="_blank">github.com/spf13/cobra</a> v1.2.1</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +36,7 @@ require (</td>
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37
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/golang/freetype@v0.0.0-20170609003504-e2365dfdc4a0" rel="nofollow noreferrer noopener" target="_blank">github.com/golang/freetype</a> v0.0.0-20170609003504-e2365dfdc4a0 // indirect</span>
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<td class="old_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
38
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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/inconshreveable/mousetrap@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">github.com/inconshreveable/mousetrap</a> v1.0.0 // indirect</span>
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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
39
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<td class="new_line diff-line-num" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/jung-kurt/gofpdf@v1.0.3-0.20190309125859-24315acbbda5" rel="nofollow noreferrer noopener" target="_blank">github.com/jung-kurt/gofpdf</a> v1.0.3-0.20190309125859-24315acbbda5 // indirect</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/klauspost/compress@v1.13.4" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/compress</a> v1.13.<span class="idiff left right">4</span> // indirect</span>
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<td class="old_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/klauspost/compress@v1.13.6" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/compress</a> v1.13.<span class="idiff left right">6</span> // indirect</span>
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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
41
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/mattn/go-runewidth@v0.0.13" rel="nofollow noreferrer noopener" target="_blank">github.com/mattn/go-runewidth</a> v0.0.13 // indirect</span>
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42
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/rivo/uniseg@v0.2.0" rel="nofollow noreferrer noopener" target="_blank">github.com/rivo/uniseg</a> v0.2.0 // indirect</span>
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43
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> <a href="https://pkg.go.dev/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bpool</a> v0.0.0-20160710042833-f9e0ee4d0403 // indirect</span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#5aa1ac64de2b0c4821af9393b44965020e4a521d"><strong>go.sum</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,7 +132,6 @@ github.com/golang/protobuf v1.4.3/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw</td>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/golang/protobuf@v1.5.0" rel="nofollow noreferrer noopener" target="_blank">github.com/golang/protobuf</a> v1.5.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/golang/protobuf@v1.5.0" rel="nofollow noreferrer noopener" target="_blank">FsONVRAS9T7sI+LIUmWTfcYkHO4aIWwzhcaSAoJOfIk=</a></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/golang/protobuf@v1.5.1" rel="nofollow noreferrer noopener" target="_blank">github.com/golang/protobuf</a> v1.5.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/golang/protobuf@v1.5.1" rel="nofollow noreferrer noopener" target="_blank">DopwsBzvsk0Fs44TXzsVbJyPhcCPeIwnvohx4u74HPM=</a></span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/golang/protobuf@v1.5.2" rel="nofollow noreferrer noopener" target="_blank">github.com/golang/protobuf</a> v1.5.2/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/golang/protobuf@v1.5.2" rel="nofollow noreferrer noopener" target="_blank">XVQd3VNwM+JqD3oG2Ue2ip4fOMUkwXdXDdiuN0vRsmY=</a></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/golang/snappy@v0.0.3" rel="nofollow noreferrer noopener" target="_blank">github.com/golang/snappy</a> v0.0.3/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/golang/snappy@v0.0.3" rel="nofollow noreferrer noopener" target="_blank">/XxbfmMg8lxefKM7IXC3fBNl/7bRcc72aCRzEWrmP2Q=</a></span>
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136
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/google/btree@v0.0.0-20180813153112-4030bb1f1f0c" rel="nofollow noreferrer noopener" target="_blank">github.com/google/btree</a> v0.0.0-20180813153112-4030bb1f1f0c/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/google/btree@v0.0.0-20180813153112-4030bb1f1f0c" rel="nofollow noreferrer noopener" target="_blank">lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=</a></span>
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137
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/google/btree@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">github.com/google/btree</a> v1.0.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/google/btree@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ=</a></span>
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138
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/google/go-cmp@v0.2.0" rel="nofollow noreferrer noopener" target="_blank">github.com/google/go-cmp</a> v0.2.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/google/go-cmp@v0.2.0" rel="nofollow noreferrer noopener" target="_blank">oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M=</a></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -201,8 +200,8 @@ github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5 h1:PJr+ZMXIecYc</td>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/jung-kurt/gofpdf@v1.0.3-0.20190309125859-24315acbbda5" rel="nofollow noreferrer noopener" target="_blank">github.com/jung-kurt/gofpdf</a> v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/jung-kurt/gofpdf@v1.0.3-0.20190309125859-24315acbbda5" rel="nofollow noreferrer noopener" target="_blank">7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes=</a></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/kisielk/errcheck@v1.5.0" rel="nofollow noreferrer noopener" target="_blank">github.com/kisielk/errcheck</a> v1.5.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/kisielk/errcheck@v1.5.0" rel="nofollow noreferrer noopener" target="_blank">pFxgyoBC7bSaBwPgfKdkLd5X25qrDl4LWUI2bnpBCr8=</a></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/kisielk/gotool@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">github.com/kisielk/gotool</a> v1.0.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/kisielk/gotool@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck=</a></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/klauspost/compress@v1.13.4" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/compress</a> v1.13.<span class="idiff left">4</span> h1:<a href="https://sum.golang.org/lookup/github.com/klauspost/compress@v1.13.4" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">0zhec2I8zGnjWcKyLl6i3gPqKANCCn5e9xmviEEeX6s</span>=</a></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/klauspost/compress@v1.13.4" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/compress</a> v1.13.<span class="idiff left">4</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/klauspost/compress@v1.13.4" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">8dP1Hq4DHOhN9w426knH3Rhby4rFm6D8eO+e+Dq5Gzg</span>=</a></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/klauspost/compress@v1.13.6" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/compress</a> v1.13.<span class="idiff left">6</span> h1:<a href="https://sum.golang.org/lookup/github.com/klauspost/compress@v1.13.6" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">P76CopJELS0TiO2mebmnzgWaajssP/EszplttgQxcgc</span>=</a></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/klauspost/compress@v1.13.6" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/compress</a> v1.13.<span class="idiff left">6</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/klauspost/compress@v1.13.6" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">/3/Vjq9QcHkK5uEr5lBEmyoZ1iFhe47etQ6QUkpK6sk</span>=</a></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/klauspost/pgzip@v1.2.5" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/pgzip</a> v1.2.5 h1:<a href="https://sum.golang.org/lookup/github.com/klauspost/pgzip@v1.2.5" rel="nofollow noreferrer noopener" target="_blank">qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE=</a></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/klauspost/pgzip@v1.2.5" rel="nofollow noreferrer noopener" target="_blank">github.com/klauspost/pgzip</a> v1.2.5/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/klauspost/pgzip@v1.2.5" rel="nofollow noreferrer noopener" target="_blank">Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs=</a></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/kortschak/utter@v0.0.0-20190412033250-50fe362e6560" rel="nofollow noreferrer noopener" target="_blank">github.com/kortschak/utter</a> v0.0.0-20190412033250-50fe362e6560/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/kortschak/utter@v0.0.0-20190412033250-50fe362e6560" rel="nofollow noreferrer noopener" target="_blank">oDr41C7kH9wvAikWyFhr6UFr8R7nelpmCF5XR5rL7I8=</a></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -245,8 +244,6 @@ github.com/pelletier/go-toml v1.9.3/go.mod h1:u1nR/EPcESfeI/szUZKdtJ0xRNbUoANCko</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pkg/errors@v0.8.1" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/errors</a> v0.8.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pkg/errors@v0.8.1" rel="nofollow noreferrer noopener" target="_blank">bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=</a></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pkg/errors@v0.9.1" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/errors</a> v0.9.1 h1:<a href="https://sum.golang.org/lookup/github.com/pkg/errors@v0.9.1" rel="nofollow noreferrer noopener" target="_blank">FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4=</a></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pkg/errors@v0.9.1" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/errors</a> v0.9.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pkg/errors@v0.9.1" rel="nofollow noreferrer noopener" target="_blank">bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=</a></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pkg/profile@v1.6.0" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/profile</a> v1.6.0 h1:<a href="https://sum.golang.org/lookup/github.com/pkg/profile@v1.6.0" rel="nofollow noreferrer noopener" target="_blank">hUDfIISABYI59DyeB3OTay/HxSRwTQ8rB/H83k6r5dM=</a></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pkg/profile@v1.6.0" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/profile</a> v1.6.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pkg/profile@v1.6.0" rel="nofollow noreferrer noopener" target="_blank">qBsxPvzyUincmltOk6iyRVxHYg4adc0OFOv72ZdLa18=</a></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pkg/sftp@v1.10.1" rel="nofollow noreferrer noopener" target="_blank">github.com/pkg/sftp</a> v1.10.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pkg/sftp@v1.10.1" rel="nofollow noreferrer noopener" target="_blank">lYOWFsE0bwd1+KfKJaKeuokY15vzFx25BLbzYYoAxZI=</a></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pmezard/go-difflib@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">github.com/pmezard/go-difflib</a> v1.0.0 h1:<a href="https://sum.golang.org/lookup/github.com/pmezard/go-difflib@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=</a></span>
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252
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/pmezard/go-difflib@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">github.com/pmezard/go-difflib</a> v1.0.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/pmezard/go-difflib@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=</a></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -261,20 +258,20 @@ github.com/rogpeppe/go-internal v1.3.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFR</td>
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/russross/blackfriday/v2@v2.0.1" rel="nofollow noreferrer noopener" target="_blank">github.com/russross/blackfriday/v2</a> v2.0.1/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/russross/blackfriday/v2@v2.0.1" rel="nofollow noreferrer noopener" target="_blank">+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=</a></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/ryanuber/columnize@v0.0.0-20160712163229-9b3edd62028f" rel="nofollow noreferrer noopener" target="_blank">github.com/ryanuber/columnize</a> v0.0.0-20160712163229-9b3edd62028f/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/ryanuber/columnize@v0.0.0-20160712163229-9b3edd62028f" rel="nofollow noreferrer noopener" target="_blank">sm1tb6uqfes/u+d4ooFouqFdy9/2g9QGwK3SQygK0Ts=</a></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/sean-/seed@v0.0.0-20170313163322-e2103e2c3529" rel="nofollow noreferrer noopener" target="_blank">github.com/sean-/seed</a> v0.0.0-20170313163322-e2103e2c3529/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/sean-/seed@v0.0.0-20170313163322-e2103e2c3529" rel="nofollow noreferrer noopener" target="_blank">DxrIzT+xaE7yg65j358z/aeFdxmN0P9QXhEzd20vsDc=</a></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.<span class="idiff left">0</span> h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.3.0" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">+QKBS2ehlQGeCmYZmr6xP8UiPdhRQI0uVH6KbYmXuIQ</span>=</a></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.<span class="idiff left">0</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.3.0" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">dl64Vmd+iK1GOMZwT7XpliFN9yTmeE9+pW7SEHEXDQQ</span>=</a></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.<span class="idiff left">1</span> h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">rdSoslv8HahfJpkzhN6W1Ky1lQ++gaBIfuJAC4f65cc</span>=</a></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bio</a> v0.3.<span class="idiff left">1</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bio@v0.3.1" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">rHA8DoaDooXKdqX7bqoksQDKm3mEAQ3MsD9nivVTSf0</span>=</a></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bpool</a> v0.0.0-20160710042833-f9e0ee4d0403 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">/3JklLnHXiWUBxWc3joQYavDQJpncRhRA909cUb7eOw=</a></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bpool</a> v0.0.0-20160710042833-f9e0ee4d0403/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bpool@v0.0.0-20160710042833-f9e0ee4d0403" rel="nofollow noreferrer noopener" target="_blank">YkgdTWfNnJgv5HVJbVSDmxQtkK3/jZWDoqcG26BVU8k=</a></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.<span class="idiff left">0</span> h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/breader@v0.3.0" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">RwAhiE8xkS4OLawSbtzP6w0KGrh6W1zmRachfzkOVPE</span>=</a></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.<span class="idiff left">0</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/breader@v0.3.0" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">dyV4ivjTV0hwP627/FQAYFgpMYEeKQYHlKs3E5iY4Dw</span>=</a></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.<span class="idiff left">1</span> h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">OjgfeHhpNGQPkS1+lgsl4eNuuO//Y16N6TkqG5oxO5U</span>=</a></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/breader</a> v0.3.<span class="idiff left">1</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/breader@v0.3.1" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">UR11JJCxU9s7eUdU4xn3L/VodxoXzWhjJPh8WZbb+us</span>=</a></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/bwt</a> v0.5.1 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/bwt@v0.5.1" rel="nofollow noreferrer noopener" target="_blank">pq9KxkJPwzUwPjwWqfTOkUmzwHm8JtMkZxBkqkzuIVo=</a></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.3.<span class="idiff left">2</span> h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">3qXkcO2erNKnPCnV8zxjN2JL5sGnOqW+muj1x4XxkuM</span>=</a></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/util</a> v0.3.<span class="idiff left">2</span>/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/util@v0.3.2" rel="nofollow noreferrer noopener" target="_blank"><span class="idiff right">pY/f5wR/0o0dJcodhw1Df/ghzqNt2wFSATW0zymI4mA</span>=</a></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/xopen</a> v0.1.0 h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">PizY52rLA7A6EdkwKZ6A8h8/a+c9DCBXqfLtwVzsWnM=</a></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shenwei356/xopen</a> v0.1.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shenwei356/xopen@v0.1.0" rel="nofollow noreferrer noopener" target="_blank">6EQUa6I7Zsl2GQKqcL9qGLrTzVE+oZyly+uhzovQYSk=</a></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="plaintext"><a href="https://pkg.go.dev/github.com/shurcooL/sanitized_anchor_name@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">github.com/shurcooL/sanitized_anchor_name</a> v1.0.0/go.mod h1:<a href="https://sum.golang.org/lookup/github.com/shurcooL/sanitized_anchor_name@v1.0.0" rel="nofollow noreferrer noopener" target="_blank">1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc=</a></span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#a02b528e8138ab6ad3eae788206eb69181c130ba"><strong>seqkit/cmd/grep.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -70,6 +70,8 @@ Attentions:</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="go"><span class="s" style="color: #d14;"> file, not the order of the query patterns. </span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="go"><span class="s" style="color: #d14;"> But for FASTA file, you can use:</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="go"><span class="s" style="color: #d14;"> seqkit faidx seqs.fasta --infile-list IDs.txt</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="go"><span class="s" style="color: #d14;"> 6. For multiple patterns, you can either set "-p" multiple times, i.e.,</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="go"><span class="s" style="color: #d14;"> -p pattern1 -p pattern2, or give a file of patterns via "-f/--pattern-file".</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="go"><span class="s" style="color: #d14;">You can specify the sequence region for searching with the flag -R (--region).</span></span>
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75
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="go"><span class="s" style="color: #d14;">The definition of region is 1-based and with some custom design.</span></span>
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<li id="32f77b9b26ba8c525e818703d5ae667b751cebef">
<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#32f77b9b26ba8c525e818703d5ae667b751cebef"><strong>seqkit/cmd/replace.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,6 +58,13 @@ Special replacement symbols (only for replacing name not sequence):</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="go"><span class="s" style="color: #d14;"> {nr} Record number, starting from 1</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="go"><span class="s" style="color: #d14;"> {kv} Corresponding value of the key (captured variable $n) by key-value file,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="go"><span class="s" style="color: #d14;"> n can be specified by flag -I (--key-capt-idx) (default: 1)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="go"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="go"><span class="s" style="color: #d14;">Special cases:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="go"><span class="s" style="color: #d14;"> 1. If replacements contain '$', </span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="go"><span class="s" style="color: #d14;"> a). If using '{kv}', you need use '$$$$' instead of a single '$':</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="go"><span class="s" style="color: #d14;"> -r '{kv}' -k <(sed 's/\$/$$$$/' kv.txt)</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="go"><span class="s" style="color: #d14;"> b). If not, use '$$':</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="go"><span class="s" style="color: #d14;"> -r 'xxx$$xx'</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="go"><span class="s" style="color: #d14;">`</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="go"> <span class="n" style="color: #333;">Run</span><span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">func</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cobra</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Command</span><span class="p">,</span> <span class="n" style="color: #333;">args</span> <span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">string</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,7 +151,7 @@ Special replacement symbols (only for replacing name not sequence):</td>
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144
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">r</span> <span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span></span>
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145
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">founds</span> <span class="p">[][][]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span></span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">found</span> <span class="p">[][]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">k</span> <span class="kt" style="color: #458; font-weight: 600;">string</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">k</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">v</span></span> <span class="kt" style="color: #458; font-weight: 600;">string</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">ok</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">doNotChange</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="go"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fastx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Record</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -198,8 +205,8 @@ Special replacement symbols (only for replacing name not sequence):</td>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ignoreCase</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="go"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ToLower</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="go"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span></span><span class="p">,</span> <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kvs</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span> <span class="n" style="color: #333;">ok</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="go"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reKV</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ReplaceAll</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">kvs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff right">]</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="go"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left right">v</span></span><span class="p">,</span> <span class="n" style="color: #333;">ok</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kvs</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span> <span class="n" style="color: #333;">ok</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="go"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reKV</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ReplaceAll</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="p">[]</span><span class="kt" style="color: #458; font-weight: 600;">byte</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">v</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keepUntouch</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="go"> <span class="n" style="color: #333;">doNotChange</span> <span class="o" style="font-weight: 600;">=</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="go"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keepKey</span> <span class="p">{</span></span>
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<li id="a081fd2a9409882bfb5fbf48cc5469d880b5a3a1">
<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#a081fd2a9409882bfb5fbf48cc5469d880b5a3a1"><strong>seqkit/cmd/subseq.go</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,13 @@ var subseqCmd = &cobra.Command{</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="go"> <span class="n" style="color: #333;">Short</span><span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"get subsequences by region/gtf/bed, including flanking sequences"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="go"> <span class="n" style="color: #333;">Long</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Sprintf</span><span class="p">(</span><span class="s" style="color: #d14;">`get subsequences by region/gtf/bed, including flanking sequences.</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="go"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="go"><span class="s" style="color: #d14;">Recommendation: use plain FASTA file, so seqkit could utilize FASTA index.</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="go"><span class="s" style="color: #d14;">Attentions:</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="go"><span class="s" style="color: #d14;"> 1. Use "seqkit grep" for extract subsets of sequences.</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="go"><span class="s" style="color: #d14;"> "seqtk subseq seqs.fasta id.txt" equals to</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="go"><span class="s" style="color: #d14;"> "seqkit grep -f id.txt seqs.fasta"</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="go"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="go"><span class="s" style="color: #d14;">Recommendation:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="go"><span class="s" style="color: #d14;"> 1. use plain FASTA file, so seqkit could utilize FASTA index.</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="go"><span class="s" style="color: #d14;">The definition of region is 1-based and with some custom design.</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="go"></span>
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<a href="https://salsa.debian.org/med-team/seqkit/-/commit/eb1d2ff15c3fa601af5cbfc7cdd1d485fda53326#48404aa0fac3725b4a485b95bf89f1b19e6da31a"><strong>seqkit/main.go</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ import (</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="go"> <span class="n" style="color: #333;">colorable</span> <span class="s" style="color: #d14;">"github.com/mattn/go-colorable"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="go"> <span class="s" style="color: #d14;">"github.com/shenwei356/go-logging"</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="go"> <span class="s" style="color: #d14;">"github.com/shenwei356/seqkit/seqkit/cmd"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="go"> <span class="s" style="color: #d14;">"github.com/shenwei356/seqkit/<span class="idiff left right">v2/</span>seqkit/cmd"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="go"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="go"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="go"><span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">logFormat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">MustStringFormatter</span><span class="p">(</span></span>
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