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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>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/nim-hts/-/commit/cf687b6b29a9546e41570b6f1bec808b36e333da">cf687b6b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-01T12:44:28+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Binary split to install testing data
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#b0b27faaec19805ecb23943d9fc1baedadcc1d67">
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+
debian/nim-hts-examples.install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/cf687b6b29a9546e41570b6f1bec808b36e333da#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" 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">@@ -20,7 +20,20 @@ Package: nim-hts-dev</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${misc:Depends}, nim</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Recommends: libhts3</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Suggests: nim-hts-examples</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: wrapper for hts C library</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> The hts library is well accepted for the handling of millions of</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> DNA sequences from what once was the high-throughput sequencing machines</span>
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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext"> in biological research and medical diagnostics/therapy control.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Package: nim-hts-examples</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Enhances: nim-hts-dev</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Description: examples for nim-hts: wrapper for hts C library</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> The hts library is well accepted for the handling of millions of</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> DNA sequences from what once was the high-throughput sequencing machines</span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="plaintext"> in biological research and medical diagnostics/therapy control.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> This package contains a test data set as well as sample scripts</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> running some test suite provided by Debian also as autopkgtest.</span></pre>
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<li id="b0b27faaec19805ecb23943d9fc1baedadcc1d67">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/cf687b6b29a9546e41570b6f1bec808b36e333da#b0b27faaec19805ecb23943d9fc1baedadcc1d67"><strong>debian/nim-hts-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">nim</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">sam</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">test_files</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">vcf</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">bcf</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">bam</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">missing</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">sources</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">unit</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="php"><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">tests</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">nim</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">hts</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nim</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/cf687b6b29a9546e41570b6f1bec808b36e333da#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">@@ -27,11 +27,9 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> nim c --nimcache:$(CURDIR)/tests/nimcache tests/all.nim</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> tests/all</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> # remnants from testing</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> rm -f ____t.vcf t.gz ti.txt.gz ti.txt.gz.csi</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> rm -f tests/run tests/HG02002.bam.csi tests/auxtest tests/newsample.vcf tests/outmissing.vcf tests/outv.vcf tests/outz.vcf tests/sample.fa.fai tests/all tests/htstest tests/bgzftest tests/bamtest</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> rm -rf tests/nimcache</span></pre>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"></span></pre>
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