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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/nim-hts">Debian Med / nim-hts</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/d7cd93e4a6b3c395e94ee17da9ce57a41a69ff45">d7cd93e4</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T10:44:57+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add watch file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/f8c670f8483142525452ab1042cc8e95a049db50">f8c670f8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T10:47:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Repack to remove binary files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/fdcfe021fa3dc13b7420a42c5e4137990bc7d527">fdcfe021</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T10:47:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3.12+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/311cd0f2be6f99d0113f00394fddaa2bb2afec10">311cd0f2</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T10:47:34+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.3.12+ds'
Update to upstream version '0.3.12+ds'
with Debian dir 43521ed649d0b5afcbe771e46b17b834ee3057f0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/fde4140377074d15fcd8c43131aff6f19df57d31">fde41403</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T11:37:34+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing sources for sourceless binaries
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/79c57baf24db2155278320533bc26706a0e047e2">79c57baf</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T11:37:56+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Regenerate repacked files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/141a330a1dd47aefc884765469a475cdd583eba2">141a330a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T11:38:29+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Disable tests for binaries which cannot be generated
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/428af9281852b4272e89305e7c4d5408ef35d666">428af928</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T11:40:30+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add upstream/metadata
</pre>
</li>
</ul>
<h4>18 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#cf9802e192b48f765b1b5c8268d550d89c933053">
<span class="new-file">
+
debian/README.source
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
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<li class="file-stats">
<a href="#579c6d41f76adf4e0f5c4023e152950c9707bcfc">
<span class="new-file">
+
debian/missing-sources/HG02002.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#b49a925cdc7b8871b76afd98af67358f6feb649c">
<span class="new-file">
+
debian/patches/disable-test-with-sourceless-file.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<span class="new-file">
+
debian/upstream/metadata
</span>
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<span class="new-file">
+
debian/watch
</span>
</a>
</li>
<li class="file-stats">
<a href="#a915d03888d528e04110fdf02f5a6b5dfcbeadd6">
<span class="deleted-file">
−
tests/HG02002.bam
</span>
</a>
</li>
<li class="file-stats">
<a href="#06383f18281b3cd96612443cfb1628c56540ed80">
<span class="deleted-file">
−
tests/HG02002.bam.bai
</span>
</a>
</li>
<li class="file-stats">
<a href="#735153dd7d01f97692567fef759354ea3c867c79">
<span class="deleted-file">
−
tests/other-for-test.bcf.csi
</span>
</a>
</li>
<li class="file-stats">
<a href="#0e1019b38d70339743eb09f5f37d9653e62fd549">
<span class="deleted-file">
−
tests/sa.bam
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b808871e61b1da6aa1c8b617d65e57e493b6c22">
<span class="deleted-file">
−
tests/sa.bam.bai
</span>
</a>
</li>
<li class="file-stats">
<a href="#007ce05f032e80925bde39662712a303c48ce5bb">
<span class="deleted-file">
−
tests/test.bcf.csi
</span>
</a>
</li>
<li class="file-stats">
<a href="#7470095d9033032fe67bf65a58a9bb8e0622ea77">
<span class="deleted-file">
−
tests/test.vcf.gz.tbi
</span>
</a>
</li>
<li class="file-stats">
<a href="#f2b258f88235f057253323c54cbc3adebddc174f">
<span class="deleted-file">
−
tests/test_files/simple.tsv.gz.csi
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="cf9802e192b48f765b1b5c8268d550d89c933053">
<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#cf9802e192b48f765b1b5c8268d550d89c933053"><strong>debian/README.source</strong></a>
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<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">
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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>
</pre>
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<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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">* tests/HG02002.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">* tests/HG02002.bam</span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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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 command:</span>
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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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">* samtools view -h -o <out>.sam <in>.bam </span>
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<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">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<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">
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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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<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"></span>
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<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">
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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/HG02002.sam | samtools view -Sb - > tests/HG02002.bam</span>
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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">* samtools index tests/HG02002.bam tests/HG02002.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"></span>
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<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">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="LC18" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sun, 01 Nov 2020 11:14:35 +0530</span>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">nim-hts (0.3.12-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">nim-hts (0.3.12<span class="idiff left right">+ds</span>-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"> * Initial release (Closes: #973510)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#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 +6,10 @@ Uploaders: Steffen Moeller <moeller@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Debian Nim Team <team+nim@tracker.debian.org></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> nim,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> libhts-dev</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> tabix,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> bcftools</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/brentp/hts-nim</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/nim-hts</span>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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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>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: nim-hts</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://github.com/brentp/hts-nim</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Files-Excluded: tests/*.bam*</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> tests/*.tbi</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> tests/test_files/*.csi</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> tests/*.csi</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">Files: *</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Copyright: 2017-2020 Brent Pedersen</span>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#579c6d41f76adf4e0f5c4023e152950c9707bcfc"><strong>debian/missing-sources/HG02002.sam</strong></a>
The diff for this file was not included because it is too large.
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<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#b49a925cdc7b8871b76afd98af67358f6feb649c"><strong>debian/patches/disable-test-with-sourceless-file.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Two binaries:</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">1. tests/other-for-test.bcf.csi - has undergone a lossy transformation and source can't be recovered</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">2. tests/test_files/simple.tsv.gz.csi - cannot be indexed properly from the existing tsv</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Hence disabled tests involving these</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Author: Nilesh Patra <npatr974@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Last-Update: 2020-11-01</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/vcftest.nim</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/vcftest.nim</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -246,10 +246,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> check variant.info.set("myflag", val) == Status.OK</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> check "myflag" notin variant.tostring()</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test "load index":</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #[test "load index":</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> var vcf:VCF</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> check open(vcf, "tests/test.bcf")</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- vcf.load_index("tests/other-for-test.bcf.csi")</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ vcf.load_index("tests/other-for-test.bcf.csi")]#</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> test "remove info from header":</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> var vcf:VCF</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/bgzftest.nim</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/bgzftest.nim</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -90,7 +90,7 @@</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> check reg == "aaa\t4\t10"</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> check found == 1</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test "bgzi-query from VCF rows":</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #[test "bgzi-query from VCF rows":</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> ## There was a discrepancy between rec.POS (int32) and BGZI.query (int64)</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> var db:BGZI</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> check db.open("tests/test_files/simple.tsv.gz")</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -102,4 +102,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> for row in db.query($rec.CHROM, rec.POS - 1, rec.POS):</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> rows.add row</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> check rows.len == 1</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- check rows[0] == "1\t10492\tC\tT"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ check rows[0] == "1\t10492\tC\tT"]#</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">dontDoNestedTests.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">disable-test-with-sourceless-file.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#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">@@ -6,6 +6,13 @@ DEB_BUILD_OPTIONS += nodoc</td>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> dh $@</span>
</pre>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
</pre>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">override_dh_auto_test:</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> # Regenerate repacked files</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> cat tests/sa.sam | samtools view -Sb - > tests/sa.bam</span>
</pre>
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<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
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> samtools index tests/sa.bam tests/sa.bam.bai</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> samtools index tests/HG02002.bam tests/HG02002.bam.bai</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> tabix tests/test.vcf.gz</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> bcftools index tests/test.bcf</span>
</pre>
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9
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> #nim c -p=/usr/share/nimble/unicodedb/ -p=/usr/share/nimble/unicodeplus/ -p=/usr/share/nimble/regex/ test/test.nim</span>
</pre>
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10
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> #nim c tests/run.nim</span>
</pre>
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11
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> #./tests/run</span>
</pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">---</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Archive: GitHub</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Bug-Database: https://github.com/brentp/hts-nim/issues</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Bug-Submit: https://github.com/brentp/hts-nim/issues/new</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Changelog: https://github.com/brentp/hts-nim/tags</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Repository: https://github.com/brentp/hts-nim.git</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Repository-Browse: https://github.com/brentp/hts-nim</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/nim-hts/-/compare/2850046bf259eb0f44931d044583d4cbb4f5a32a...428af9281852b4272e89305e7c4d5408ef35d666#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%,repacksuffix=+ds,dversionmangle=auto" \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">https://github.com/brentp/hts-nim/releases .*/archive/v?@ANY_VERSION@\.tar\.gz</span></pre>
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