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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/pyranges">Debian Med / pyranges</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyranges/-/commit/f49182c8f093bda0efd57f5c5f812b9a7bc31677">f49182c8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-06-21T20:13:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Readme for missing sources
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyranges/-/commit/739fd4160324feeed368d4eaa7a52a6494bde31a">739fd416</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-06-21T20:14:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not install binaries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pyranges/-/commit/32b41b1fb93c50e75cbae7e7f42ad1acb8a09174">32b41b1f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-06-21T20:15:15+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
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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="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/pyranges/-/compare/f16a1c93c262892ce4134072d4ca93e26591f4df...32b41b1fb93c50e75cbae7e7f42ad1acb8a09174#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/test_data/test_sorted.bam.bai </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* tests/test_data/test_sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">* pyranges/example_data/control.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">* pyranges/example_data/control.bam</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" 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="LC9" class="line" lang="plaintext">* samtools view -h -o test_sorted.sam test_sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">* samtools view -h -o control.sam control.bam</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">And the corresponding *.sam files are added to: debian/missing-sources</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">They can be generated back with the following commands:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">* cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">* cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">* samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">* samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" 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="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sun, 21 Jun 2020 20:13:10 +0530</span></pre>
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<a href="https://salsa.debian.org/med-team/pyranges/-/compare/f16a1c93c262892ce4134072d4ca93e26591f4df...32b41b1fb93c50e75cbae7e7f42ad1acb8a09174#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">pyranges (0.0.79+ds-1) UNRELEASED; urgency=medium</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"> [ Steffen Moeller, Nilesh Patra ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Initial release (Closes: #963015)</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="LC5" class="line" lang="plaintext"> TODO: Waiting for python3-pyrle</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"> -- Steffen Moeller <moeller@debian.org> Wed, 17 Jun 2020 20:08:00 +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sun, 21 Jun 2020 20:13:10 +0530</span></pre>
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<a href="https://salsa.debian.org/med-team/pyranges/-/compare/f16a1c93c262892ce4134072d4ca93e26591f4df...32b41b1fb93c50e75cbae7e7f42ad1acb8a09174#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -21,3 +21,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> find debian/ -name *.bam* | xargs rm -rf</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> find debian/ -name 'hi' | xargs rm -rf</span></pre>
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