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GitLab

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<h3>

Steffen Möller pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8">b1deb8e9</a></strong>

<div>

<span>by Steffen Möller</span>

<i>at 2020-11-02T21:36:31+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Partial packaging - still missing deps

</pre>

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</ul>

<h4>7 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

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+

debian/changelog

</span>

</a>

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<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

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+

debian/control

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<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

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+

debian/copyright

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</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

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+

debian/rules

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<li class="file-stats">

<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

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+

debian/salsa-ci.yml

</span>

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<li class="file-stats">

<a href="#53399f7f2dd7535c43cdcfa511a9c06044a9c238">

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+

debian/source/format

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<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

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+

debian/watch

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<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hts-nim-tools (0.2.0-1) UNRELEASED; urgency=medium</span>

</pre>

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2

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

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Initial release (Closes: #973650)</span>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    Misses brentp's nim modules lapper and kexec</span>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org>  Mon, 02 Nov 2020 20:26:54 +0100</span></pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: hts-nim-tools</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Section: science</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Priority: optional</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Maintainer: Steffen Moeller <moeller@debian.org></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">               nim,</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">               nim-hts-dev,</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">               nim-docopt-dev,</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">               nim-unicodedb-dev,</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">               nim-unicodeplus-dev,</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">               nim-regex-dev</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.5.0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Homepage: https://github.com/brentp/hts-nim-tools</span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/hts-nim-tools</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/hts-nim-tools.git</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Rules-Requires-Root: no</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Package: hts-nim-tools</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Architecture: any</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Description: tools biological sequences: bam-filter, count-reads, vcf-check</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> This package provides several tools that (at least at the time of their creation)</span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> provide functionalities beyond the routine provided by samtools and other reverse</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dependencies of the htslib.</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> .</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> These new tools are</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">  • bam-filter    : filter BAM/CRAM/SAM files with a simple expression language</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">  • count-reads   : count BAM/CRAM reads in regions given in a BED file</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">  • vcf-check     : check regions of a VCF against a background for missing chunks</span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> .</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> and yes, as the name suggests, these tools are all implemented in nim, using the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> nim-hts (upstream: hts-nim) wrapper for the htslib.</span></pre>

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<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: hts-nim-tools</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: https://github.com/brentp/hts-nim-tools</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files: *</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Copyright: 2018 Brent Pedersen <@brentp></span>

</pre>

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

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

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">License: MIT</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Files: debian/*</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Copyright: 2020 Steffen Moeller <moeller@debian.org></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: MIT</span>

</pre>

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

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

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: MIT</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining a</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> copy of this software and associated documentation files (the "Software"),</span>

</pre>

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</td>

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

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> to deal in the Software without restriction, including without limitation</span>

</pre>

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</td>

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> the rights to use, copy, modify, merge, publish, distribute, sublicense,</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> and/or sell copies of the Software, and to permit persons to whom the</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Software is furnished to do so, subject to the following conditions:</span>

</pre>

</td>

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

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> .</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> The above copyright notice and this permission notice shall be included</span>

</pre>

</td>

</tr>

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</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> in all copies or substantial portions of the Software.</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> .</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS</span>

</pre>

</td>

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

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

</td>

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

25

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF</span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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

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

</td>

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

1

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">export DH_VERBOSE = 1</span>

</pre>

</td>

</tr>

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

</td>

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

3

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

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

</td>

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

4

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">%:</span>

</pre>

</td>

</tr>

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

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

</td>

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

5

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">      dh $@</span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

</td>

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

7

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">override_dh_auto_build:</span>

</pre>

</td>

</tr>

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

</td>

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

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">      # needs kexpr</span>

</pre>

</td>

</tr>

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

</td>

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

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      #nim c -p:/usr/share/nimble/unicodeplus  -p:/usr/share/nimble/unicodedb  -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt  -p:/usr/share/nimble/hts src/bam_filter.nim</span>

</pre>

</td>

</tr>

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

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

</td>

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

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">     # nim c -p:/usr/share/nimble/unicodeplus  -p:/usr/share/nimble/unicodedb  -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt  -p:/usr/share/nimble/hts src/hts_nim_tools.nim</span>

</pre>

</td>

</tr>

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

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

</td>

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

11

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">     # needs lapper</span>

</pre>

</td>

</tr>

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

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">     # nim c -p:/usr/share/nimble/unicodeplus  -p:/usr/share/nimble/unicodedb  -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt  -p:/usr/share/nimble/hts src/count_reads.nim</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">     # nim c -p:/usr/share/nimble/unicodeplus  -p:/usr/share/nimble/unicodedb  -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt  -p:/usr/share/nimble/hts src/copy_number_sampler.nim</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">     # works!</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">     nim c -p:/usr/share/nimble/unicodeplus  -p:/usr/share/nimble/unicodedb  -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt  -p:/usr/share/nimble/hts src/vcf_check.nim</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">override_dh_auto_clean:</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">     rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads</span>

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

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</li>

<li id="b1dbf22e88351ec0d5d1d1a7f53295504b480e61">

<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># For more information on what jobs are run see:</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># https://salsa.debian.org/salsa-ci-team/pipeline</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># To enable the jobs, go to your repository (at salsa.debian.org)</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># and click over Settings > CI/CD > Expand (in General pipelines).</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># In "Custom CI config path" write debian/salsa-ci.yml and click</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># in "Save Changes". The CI tests will run after the next commit.</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>

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<br>

</li>

<li id="53399f7f2dd7535c43cdcfa511a9c06044a9c238">

<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>

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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b1deb8e91ec0e64e5f611bfbc35085691aab81c8#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%hts-nim-tools-$1.tar.gz%" \</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">   https://github.com/brentp/hts-nim-tools/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></pre>

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