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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/hts-nim-tools">Debian Med / hts-nim-tools</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b9f81a0cd792c907e29015a7448453ea56354f5a">b9f81a0c</a></strong>
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<span>by Steffen Möller</span>
<i>at 2020-11-07T21:03:15+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Now lintian-clean, except for missing man page
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#ba6fbe753a5282e2b08c3ca9bf7f2b1467d4474e">
debian/hts-nim-tools.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/hts-nim-tools/-/commit/b9f81a0cd792c907e29015a7448453ea56354f5a#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">@@ -22,14 +22,14 @@ Package: hts-nim-tools</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: tools biological sequences: bam-filter, count-reads, vcf-check</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> This package provides several tools that (at least at the time of their<span class="idiff left right"> creation)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> <span class="idiff left right">provide functionalities beyond the routine provided by samtools and other reverse</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> dependencies of the htslib.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> This package provides several tools that (at least at the time of their</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> <span class="idiff left right">creation) provide functionalities beyond the routine provided by samtools</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> <span class="idiff left right">and other reverse </span>dependencies of the htslib.</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"> These new tools are</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> • bam-filter <span class="idiff left right"> </span>: filter BAM/CRAM/SAM files with a simple expression language</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> • count-reads<span class="idiff left right"> </span>: count BAM/CRAM reads in regions given in a BED file</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> • vcf-check <span class="idiff left right"> </span>: check regions of a VCF against a background for missing chunks</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> • bam-filter : filter BAM/CRAM/SAM files with a simple expression language</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> • count-reads: count BAM/CRAM reads in regions given in a BED file</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> • vcf-check : check regions of a VCF against a background for missing chunks</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> and yes, as the name suggests, these tools are all implemented in nim,<span class="idiff left right"> using the</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> nim-hts (upstream: hts-nim) wrapper for the htslib.</span></pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> and yes, as the name suggests, these tools are all implemented in nim,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> <span class="idiff left right">using the </span>nim-hts (upstream: hts-nim) wrapper for the htslib.</span></pre>
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<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b9f81a0cd792c907e29015a7448453ea56354f5a#ba6fbe753a5282e2b08c3ca9bf7f2b1467d4474e"><strong>debian/hts-nim-tools.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;"><span class="idiff left">src</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff right">hts_nim_tools</span></span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;"><span class="idiff left">bin</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">/*</span></span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/b9f81a0cd792c907e29015a7448453ea56354f5a#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">@@ -7,13 +7,17 @@ NIMCACHE=$(CURDIR)/nimcache</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/kexpr -p:/usr/share/nimble/hts src/bam_filter.nim</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/hts src/count_reads.nim</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/copy_number_sampler.nim</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/kexpr -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/hts_nim_tools.nim</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> #nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/hts src/vcf_check.nim</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> #nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/kexpr -p:/usr/share/nimble/hts src/bam_filter.nim</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> #nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/hts src/count_reads.nim</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> #nim c --nimcache:$(NIMCACHE) -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/copy_number_sampler.nim</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> nim c --debuginfo:on --nimcache:$(NIMCACHE) --out:bin/hts-nim-tools -p:/usr/share/nimble/unicodeplus -p:/usr/share/nimble/unicodedb -p:/usr/share/nimble/regex -p:/usr/share/nimble/docopt -p:/usr/share/nimble/lapper -p:/usr/share/nimble/kexpr -p:/usr/lib/nim/pure -p:/usr/share/nimble/hts src/hts_nim_tools.nim</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">override_dh_dwz:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> echo "I: not executing dwz, which fails because of Unknown DWARF DW_OP_0"</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<td class="diff-line-num 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">
20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> rm -f src/version src/vcf_check src/bam_filter src/hts_nim_tools src/count_reads src/copy_number_sampler</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">
18
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<td class="diff-line-num new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> rm -rf $(NIMCACHE)</span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> rm -rf bin</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">
19
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<td class="diff-line-num new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span></pre>
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