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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/vcfanno">Debian Med / vcfanno</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcfanno/-/commit/47d537764b09929dc25e6671d867ffea6f7cf7c1">47d53776</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-18T04:30:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install directories by names to avoid confusion
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcfanno/-/commit/3102310831f3bda4e2e59fcc9bf401b47acc0751">31023108</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-07-18T04:31:12+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcfanno/-/commit/ecfc8be651357969c7e833349d976d1f608f06b1">ecfc8be6</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-07-18T04:35:04+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add information about missing bam file
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<h4>3 changed files:</h4>
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<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
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+
debian/README.source
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#c9be55b34d5aff561f9a9608d673a8b7046b584a">
debian/vcfanno-examples.docs
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<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/vcfanno/-/compare/dc865e05d2c0eda4bf1c13c05db275351eff657a...ecfc8be651357969c7e833349d976d1f608f06b1#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Upstream provides binary files without sources for:</span>
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<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">* example/ex.bam </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* example/ex.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">These have been converted to corresponding text (.sam) files with the commands:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">* samtools view -h -o ex.sam example/ex.bam </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">And the corresponding *.sam files are added to: debian/missing-sources</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">They can be generated back with the following commands:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">* cat debian/missing-sources/ex.sam| samtools view -Sb - > example/ex.bam</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">* samtools index data/ex.bam data/ex.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">These commands are also being run in debian/rules since these binaries are needed for testing.</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"> -- Nilesh Patra <npatra974@gmail.com> Sat, 18 Jul 2020 04:33:13 +0530</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/vcfanno/-/compare/dc865e05d2c0eda4bf1c13c05db275351eff657a...ecfc8be651357969c7e833349d976d1f608f06b1#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="idiff left right">vcfanno</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,8 +11,18 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-<span class="idiff left">a</span></span><span class="idiff"> /usr/share/doc/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff right">/</span>examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-<span class="idiff left">Rf</span></span><span class="idiff"> /usr/share/doc/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="nt" style="color: #000080;"><span class="idiff right">-</span>examples</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">vcfanno <span class="nt" style="color: #000080;">-base-path</span> tests/data/ <span class="nt" style="color: #000080;">-lua</span> example/custom.lua tests/data/number.conf tests/data/number-input.vcf</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-c</span> <span class="s2" style="color: #d14;">"lua error in postannotation"</span> <span class="nv" style="color: #008080;">$STDERR_FILE</span><span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">!=</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">exit </span>1</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$STDERR_FILE</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">vcfanno tests/overwrite-multiple-alts/b/conf.toml tests/overwrite-multiple-alts/b/input.vcf</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"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/vcfanno/-/compare/dc865e05d2c0eda4bf1c13c05db275351eff657a...ecfc8be651357969c7e833349d976d1f608f06b1#c9be55b34d5aff561f9a9608d673a8b7046b584a"><strong>debian/vcfanno-examples.docs</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">example<span class="idiff left right">/*</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">tests<span class="idiff left right">/*</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">example</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">tests</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">debian/missing-sources/*</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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