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<h3>
Steffen Möller 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/2850046bf259eb0f44931d044583d4cbb4f5a32a">2850046b</a></strong>
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<span>by Steffen Möller</span>
<i>at 2020-11-01T05:29:20+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Addressed hickups for tests in cowbuilder
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<h4>4 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="#6b8d197783f5667cc5371b5e0153267f92c5f6e6">
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+
debian/patches/dontDoNestedTests.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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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/2850046bf259eb0f44931d044583d4cbb4f5a32a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" 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">@@ -5,7 +5,8 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Uploaders: Steffen Moeller <moeller@debian.org>,</span>
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> Debian Nim Team <team+nim@tracker.debian.org></span>
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<td class="diff-line-num new_line" data-linenumber="7" 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="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="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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<td class="diff-line-num old_line" data-linenumber="9" 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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<td class="diff-line-num new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: https://github.com/brentp/hts-nim</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/nim-hts</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="15" 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">@@ -14,7 +15,8 @@ Rules-Requires-Root: no</td>
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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">Package: nim-hts-dev</span>
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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Depends: ${misc:Depends}, nim, nim-unicodedb-dev, nim-unicodeplus-dev</span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="plaintext">Depends: ${misc:Depends}, nim</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext">Recommends: libhts3</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC20" class="line" lang="plaintext">Description: wrapper for hts C library</span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="LC21" class="line" lang="plaintext"> The hts library is well accepted for the handling of millions of</span>
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<td class="diff-line-num new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> DNA sequences from what once was the high-throughput sequencing machines</span>
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<li id="6b8d197783f5667cc5371b5e0153267f92c5f6e6">
<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/2850046bf259eb0f44931d044583d4cbb4f5a32a#6b8d197783f5667cc5371b5e0153267f92c5f6e6"><strong>debian/patches/dontDoNestedTests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: nim-hts/tests/all.nim</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- nim-hts.orig/tests/all.nim</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ nim-hts/tests/all.nim</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,2 +1,2 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> {. warning[UnusedImport]:off .}</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import flagtest, cigartest, htstest, bgzftest, faitest, auxtest, vcftest, bamtest, statstests, vcfiso, test_files, test_readme</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import flagtest, cigartest, htstest, bgzftest, faitest, auxtest, vcftest, bamtest, statstests, vcfiso, test_files</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/2850046bf259eb0f44931d044583d4cbb4f5a32a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">dontDoNestedTests.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/nim-hts/-/commit/2850046bf259eb0f44931d044583d4cbb4f5a32a#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">@@ -17,7 +17,7 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> #tests/bamtest</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> #nim c tests/bgzftest.nim</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> #tests/bgzftest</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> nim c tests/all.nim</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> nim c <span class="idiff left right">--nimcache:$(CURDIR)/tests/nimcache </span>tests/all.nim</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> tests/all</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"></span>
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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">@@ -25,6 +25,6 @@ override_dh_auto_clean:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> # remnants from testing</span>
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<pre style="margin: 0;"> <span id="LC27" 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="LC28" 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</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="LC28" 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<span class="idiff left right"> tests/all tests/htstest tests/bgzftest tests/bamtest</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> rm -rf tests/nimcache</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span></pre>
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