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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/allelecount">Debian Med / allelecount</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/a346e7453cb681efbbb4378a8fe3bec60c99c1cc">a346e745</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-12T11:20:10+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Conda ID
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<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/e3f44a9c9627a27df84f7fde78f8889fe86f1e52">e3f44a9c</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-05-12T11:30:33+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide separate Perl module package
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#cd5da5bacfff6fb209a768e570561156b0383249">
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debian/allelecount.install
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#1858c34cae4c5f51ec5035b1d447e13c7a83cb00">
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+
debian/liballelecount-perl.install
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<li class="file-stats">
<a href="#1c37626201ffec70e15c41643c0f96522b900c98">
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debian/liballelecount-perl.lintian-overrides
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="cd5da5bacfff6fb209a768e570561156b0383249">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52#cd5da5bacfff6fb209a768e570561156b0383249"><strong>debian/allelecount.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">c</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">alleleCounter</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,6 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libbz2-dev,</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" 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">@@ -23,7 +24,19 @@ Homepage: https://github.com/cancerit/alleleCount</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Package: allelecount</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ${misc:Depends}</span>
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<td class="diff-line-num new new_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext">Description: NGS copy number algorithms</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> Support code for NGS copy number algorithms. Takes a file of locations</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> and a [cr|b]am file and generates a count of coverage of each allele</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> [ACGT] at that location (given any filter settings).</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> The alleleCount package primarily exists to prevent code duplication</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> between some other projects, specifically AscatNGS and Battenberg.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Package: liballelecount-perl</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Section: perl</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> ${perl:Depends},</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> libconst-fast-perl,</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> libdevel-cover-perl,</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">@@ -33,10 +46,13 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> libpod-coverage-perl,</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> libtest-fatal-perl (>= 0.013),</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> libtry-tiny-perl</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">Description: NGS copy number algorithms</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Description: <span class="idiff left right">Perl interface to </span>NGS copy number algorithms</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> Support code for NGS copy number algorithms. Takes a file of locations</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> and a [cr|b]am file and generates a count of coverage of each allele</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> [ACGT] at that location (given any filter settings).</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> The alleleCount package primarily exists to prevent code duplication</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"> between some other projects, specifically AscatNGS and Battenberg.</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> This package provided the Perl interface to alleleCounter providing</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> Sanger::CGP::AlleleCount::Genotype.</span></pre>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52#1858c34cae4c5f51ec5035b1d447e13c7a83cb00"><strong>debian/liballelecount-perl.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span></span></pre>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52#1c37626201ffec70e15c41643c0f96522b900c98"><strong>debian/liballelecount-perl.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">libalelecounter-perl: script-with-language-extension usr/bin/*.*</span></pre>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52#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">@@ -9,7 +9,7 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></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"> dh $@<span class="idiff left right"> --sourcedirectory=c</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> dh $@</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">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh_auto_clean --sourcedirectory=c</span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/compare/9d13d8f17db49f754b389b94d8e3a7ec3cf70b80...e3f44a9c9627a27df84f7fde78f8889fe86f1e52#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Author: </span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Title: </span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Journal: </span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Year: </span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Volume: </span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Number: </span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Pages: </span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> DOI: </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> PMID:</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> URL: </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> eprint: </span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Entry: cancerit-allelecount</span></pre>
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