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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqkit">Debian Med / seqkit</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/4b78cfdf2ac8f3398b7d771c140c5335cf46833f">4b78cfdf</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-03T23:09:11+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Information on repacked bam files
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/seqkit/-/commit/893fc0e19772be089f4370ec99f9cf4b76f1f6cc">893fc0e1</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-08-03T23:10:52+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add information about test
</pre>
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<h4>2 changed files:</h4>
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<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
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debian/README.source
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debian/README.test
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<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/seqkit/-/compare/edacb01b1eae42e2b35167998975ec5a497a78c7...893fc0e19772be089f4370ec99f9cf4b76f1f6cc#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">* tests/pcs109_5k_prim.sam </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* tests/pcs109_5k.sam</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">* tests/pcs109_5k_spliced.sam</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">These have been converted to corresponding text (.sam) files with command:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">* samtools view -h -o <out>.sam <in>.bam </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">They can be generated back with the following commands:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">* cat debian/missing-sources/pcs109_5k_prim.sam | samtools view -Sb - > tests/pcs109_5k_prim.bam</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">* cat debian/missing-sources/pcs109_5k.sam | samtools view -Sb - > tests/pcs109_5k.bam</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">* cat debian/missing-sources/pcs109_5k_spliced.sam | samtools view -Sb - > tests/pcs109_5k_spliced.bam</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">* samtools index tests/pcs109_5k_prim.bam tests/pcs109_5k_prim.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">* samtools index tests/pcs109_5k.bam tests/pcs109_5k.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">* samtools index tests/pcs109_5k_spliced.bam tests/pcs109_5k_spliced.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">These commands are also being run in debian/rules since these binaries are needed for autopkgtests.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Mon, 03 Aug 2020 21:49:28 +0530</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/seqkit/-/compare/edacb01b1eae42e2b35167998975ec5a497a78c7...893fc0e19772be089f4370ec99f9cf4b76f1f6cc#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"></span></pre>
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