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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/bamkit">Debian Med / bamkit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/228a31b66caa2ae2c7442410f5bea616b5fb7de8">228a31b6</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T00:55:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add python3-pysam to Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/159db09dfad85745aeea495af269787b2e932475">159db09d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T00:55:42+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Declare compliance with policy 4.5.1
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/2142c6e0d9acc3ef881ac22e5edb75c70713543c">2142c6e0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T00:56:18+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor fix
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/bamkit/-/commit/a4c1b3ec1cf80f27f6109762d2084a9b3d8cfe95">a4c1b3ec</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-05T00:57:17+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e4786063b10c090a5cffb0b0ed438b8a526a51d1...a4c1b3ec1cf80f27f6109762d2084a9b3d8cfe95#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">bamkit (0.0.1+git20170413.ccd079d-3) UNRELEASED; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> [ Shruti Sridhar ]</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Add autopkgtests</span>
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<td class="old_line diff-line-num" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Install docs</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Shruti Sridhar <shruti.sridhar99@gmail.com> Wed, 04 Aug 2021 23:39:29 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Add python3-pysam to Depends</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Declare compliance with policy 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Thu, 05 Aug 2021 00:56:34 +0530</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">bamkit (0.0.1+git20170413.ccd079d-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e4786063b10c090a5cffb0b0ed438b8a526a51d1...a4c1b3ec1cf80f27f6109762d2084a9b3d8cfe95#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -6,7 +6,7 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bamkit</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bamkit.git</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://github.com/hall-lab/bamkit</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">@@ -15,7 +15,8 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: bamkit</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python3-pysam</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Description: tools for common BAM file manipulations</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> This package provides some Python3 tools for common BAM file</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> manipulations.</span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e4786063b10c090a5cffb0b0ed438b8a526a51d1...a4c1b3ec1cf80f27f6109762d2084a9b3d8cfe95#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, <span class="idiff left right">python3-pysam, </span>samtools</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, samtools</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/bamkit/-/compare/e4786063b10c090a5cffb0b0ed438b8a526a51d1...a4c1b3ec1cf80f27f6109762d2084a9b3d8cfe95#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -23,5 +23,5 @@ samtools addreplacerg -r ID:S1 -r LB:L1 -r SM:SAMPLE1 -o output reads.bam</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell">bamlibs.py reads.bam </span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell">bamcleanheader.py reads.bam <span class="o" style="font-weight: 600;">></span> output</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell">bamfilterrg.py <span class="nt" style="color: #000080;">-i</span> reads.bam <span class="o" style="font-weight: 600;">></span> filter</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"output"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"filter"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1<span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff right">"PASS Tests"</span></span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"output"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"filter"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS Tests"</span></span></pre>
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