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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/allelecount">Debian Med / allelecount</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189">77e90fde</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-21T17:29:52+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.2.1</pre>
</li>
</ul>
<h4>19 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
</a>
</li>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#e966165f0c7a7bd4a653a7e55ad979fea5be3a90">
build/opt-build.sh
</a>
</li>
<li class="file-stats">
<a href="#8b9e8f1124050d1793c0beca78d203228ec949ca">
c/src/alleleCounter.c
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</li>
<li class="file-stats">
<a href="#e48e40052652e64de8f1b45c47565b343b77ebcf">
c/src/bam_access.c
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</li>
<li class="file-stats">
<a href="#55adaf5fef8455960a1f0d4a76bbd6d50c471267">
c/src/bam_access.h
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<li class="file-stats">
<a href="#a155a9ca246a73bebef0c2f24aaa5caa21be38c2">
c/tests/bam_access_tests.c
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<li class="file-stats">
<a href="#f65782c608e1cad8f0405797c356fc8016fa46d1">
c/tests/minunit.h
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<li class="file-stats">
<a href="#c4553b09bd8cb4bb87239a3d3bb9a84e38d9d7c2">
c/tests/runtests.sh
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<li class="file-stats">
<a href="#31355477081907f59eb87bc628b4e3a7c370e451">
perl/Makefile.PL
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<li class="file-stats">
<a href="#4d78a438d73857820bc8ea5b4470a117b56e5f8a">
perl/bin/alleleCounter.pl
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<li class="file-stats">
<a href="#027f40d8d7bccd8caf08a7236885032f188780c1">
perl/lib/Sanger/CGP/AlleleCount.pm
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<li class="file-stats">
<a href="#d07b67fccf1ea50b9817db5a04f530385be5c808">
perl/lib/Sanger/CGP/AlleleCount/Genotype.pm
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<li class="file-stats">
<a href="#3aac7ffa1f2918a9dc1e8a379d762d892b207b9f">
perl/t/1_pm_compile.t
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<li class="file-stats">
<a href="#060cf87839203496796c248124853fe18431aab7">
perl/t/2_pl_compile.t
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<li class="file-stats">
<a href="#0253730b599615614b44f25db771a896d6f4809f">
perl/t/genotype.t
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<li class="file-stats">
<a href="#ce2209c3363c413f1acd1a7698a221ee5358c8ac">
prerelease.sh
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<li class="file-stats">
<a href="#592a1aae25926e838f4bca2e1c8981f30b077dda">
setup.sh
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># CHANGES</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## v4.2.1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="markdown"><span class="p">*</span> Update so docker and native install use same install scripts behind the scenes</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="markdown"><span class="p">*</span> Docker now actually has htslib 1.11</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="markdown"><span class="p">*</span> htslib compiled with libdeflate for improved performance</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="markdown"></span>
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## v4.2.0</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></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="markdown"><span class="p">*</span> Updated to hstlib 1.11</span>
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<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:<span class="idiff left right">16</span>.04 as builder</span></span>
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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="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:<span class="idiff left right">20</span>.04 as builder</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="docker"></span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">USER</span><span class="s" style="color: #d14;"> root</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># ALL tool versions used by opt-build.sh</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> VER_HTSLIB="1.7"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># need to keep in sync with setup.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> VER_HTSLIB="1.11"</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> VER_LIBDEFLATE="v1.6"</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nt" style="color: #000080;">-yq</span> update</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="docker">build-essential <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="docker">apt-transport-https <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="docker">curl <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="docker">ca-certificates <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="docker">make <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="docker">bzip2 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="docker">gcc <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="docker">locales <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="docker">curl <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="docker">wget <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="docker">libtasn1-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="docker">libgnutls-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="docker">nettle-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="docker">libgmp-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="docker">libp11-kit-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="docker">zlib1g-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="docker">libbz2-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="docker">liblzma-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="docker">libcurl4-gnutls-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="docker">libncurses5-dev</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> build-essential</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> apt-transport-https</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> curl</span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> ca-certificates</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> make</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> bzip2</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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> gcc</span>
</pre>
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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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> locales</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> curl</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> wget</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> libtasn1-dev</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> nettle-dev</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> libgmp-dev</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> libp11-kit-dev</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> zlib1g-dev</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> libbz2-dev</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> liblzma-dev</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> libcurl4-gnutls-dev</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-yq</span> <span class="nt" style="color: #000080;">--no-install-recommends</span> libncurses5-dev</span>
</pre>
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30
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>locale-gen en_US.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>update-locale <span class="nv" style="color: #008080;">LANG</span><span class="o" style="font-weight: 600;">=</span>en_US.UTF-8</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">@@ -46,11 +47,10 @@ RUN bash build/opt-build.sh $OPT</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="docker"><span class="k" style="font-weight: 600;">COPY</span><span class="s" style="color: #d14;"> . .</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>bash build/opt-build-local.sh <span class="nv" style="color: #008080;">$OPT</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="docker"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:<span class="idiff left right">16</span>.04</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:<span class="idiff left right">20</span>.04</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="docker"><span class="k" style="font-weight: 600;">LABEL</span><span class="s" style="color: #d14;"> maintainer="cgphelp@sanger.ac.uk" \</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="docker"> uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="docker"> version="v1.0.0" \</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="docker"> description="alleleCount docker"</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nt" style="color: #000080;">-yq</span> update</span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -125,7 +125,7 @@ The docker images are know to work correctly after import into a singularity ima</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## LICENCE</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="markdown">Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown">Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="markdown">Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#e966165f0c7a7bd4a653a7e55ad979fea5be3a90"><strong>build/opt-build.sh</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">@@ -49,19 +49,33 @@ export MANPATH=`echo $INST_PATH/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PERL5LIB</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$INST_PATH</span>/lib/perl5:<span class="nv" style="color: #008080;">$PERL5LIB</span> | perl <span class="nt" style="color: #000080;">-pe</span> <span class="s1" style="color: #d14;">'s/:\$//;'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-u</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## grab cpanm </span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell">curl <span class="nt" style="color: #000080;">-L</span> http://cpanmin.us | perl - App::cpanminus</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="shell"><span class="nv" style="color: #008080;">CPANM</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>which cpanm<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## INSTALL CPANMINUS</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell">curl <span class="nt" style="color: #000080;">-sSL</span> https://cpanmin.us/ <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/cpanm</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell">perl <span class="nv" style="color: #008080;">$SETUP_DIR</span>/cpanm <span class="nt" style="color: #000080;">--no-wget</span> <span class="nt" style="color: #000080;">--no-interactive</span> <span class="nt" style="color: #000080;">--notest</span> <span class="nt" style="color: #000080;">--mirror</span> http://cpan.metacpan.org <span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$INST_PATH</span> App::cpanminus</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/cpanm</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Installing Perl base deps ..."</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/basePerlDeps.success <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">perlmods</span><span class="o" style="font-weight: 600;">=(</span> <span class="s2" style="color: #d14;">"ExtUtils::CBuilder"</span> <span class="s2" style="color: #d14;">"Module::Build~0.42"</span> <span class="s2" style="color: #d14;">"Const::Fast"</span> <span class="s2" style="color: #d14;">"File::Which"</span> <span class="s2" style="color: #d14;">"LWP::UserAgent"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">perlmods</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="shell"> <span class="nv" style="color: #008080;"><span class="idiff left right">$CPANM</span></span> <span class="nt" style="color: #000080;">--no-interactive</span> <span class="nt" style="color: #000080;">--notest</span> <span class="nt" style="color: #000080;">--mirror</span> http://cpan.metacpan.org <span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$INST_PATH</span> <span class="nv" style="color: #008080;">$i</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="idiff left right">cpanm</span> <span class="nt" style="color: #000080;">--no-interactive</span> <span class="nt" style="color: #000080;">--notest</span> <span class="nt" style="color: #000080;">--mirror</span> http://cpan.metacpan.org <span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$INST_PATH</span> <span class="nv" style="color: #008080;">$i</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">touch</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/basePerlDeps.success</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## libdeflate</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/libdeflate.success <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> tmp_deflate</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> tmp_deflate</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"> curl <span class="nt" style="color: #000080;">-sSL</span> <span class="nt" style="color: #000080;">--retry</span> 10 https://github.com/ebiggers/libdeflate/archive/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VER_LIBDEFLATE</span><span class="k" style="font-weight: 600;">}</span>.tar.gz <span class="o" style="font-weight: 600;">></span> distro.tar.gz</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">--strip-components</span> 1 <span class="nt" style="color: #000080;">-C</span> tmp_deflate <span class="nt" style="color: #000080;">-zxf</span> distro.tar.gz</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd </span>tmp_deflate</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"> <span class="nv" style="color: #008080;">PREFIX</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span> make <span class="nt" style="color: #000080;">-j</span><span class="nv" style="color: #008080;">$CPU</span> <span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-fPIC -O3"</span> <span class="nb" style="color: #0086b3;">install</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> cd</span> ../</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> distro.<span class="k" style="font-weight: 600;">*</span> tmp_deflate</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">touch</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/libdeflate.success</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"></span>
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65
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"><span class="nv" style="color: #008080;">SOURCE_HTSLIB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"https://github.com/samtools/htslib/releases/download/</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VER_HTSLIB</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/htslib-</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VER_HTSLIB</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.tar.bz2"</span></span>
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66
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"></span>
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67
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" 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="92" 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">@@ -78,7 +92,9 @@ if [ ! -e $SETUP_DIR/htslib.success ]; then</td>
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78
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> htslib</span>
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79
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">--strip-components</span> 1 <span class="nt" style="color: #000080;">-C</span> htslib <span class="nt" style="color: #000080;">-jxf</span> htslib-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VER_HTSLIB</span><span class="k" style="font-weight: 600;">}</span>.tar.bz2</span>
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80
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd </span>htslib</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="shell"> ./configure <span class="nt" style="color: #000080;">--enable-plugins</span> <span class="nt" style="color: #000080;">--enable-libcurl</span> <span class="nt" style="color: #000080;">--prefix</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"> ./configure <span class="nt" style="color: #000080;">--enable-plugins</span> <span class="nt" style="color: #000080;">--enable-libcurl</span> <span class="nt" style="color: #000080;">--with-libdeflate</span> <span class="nt" style="color: #000080;">--prefix</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span> <span class="se" style="color: #d14;">\</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"> <span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-I</span><span class="nv" style="color: #008080;">$INST_PATH</span><span class="s2" style="color: #d14;">/include"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"> <span class="nv" style="color: #008080;">LDFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-L</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INST_PATH</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/lib -Wl,-R</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">INST_PATH</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/lib"</span></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="shell"> make <span class="nt" style="color: #000080;">-j</span><span class="nv" style="color: #008080;">$CPU</span></span>
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83
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="shell"> make <span class="nb" style="color: #0086b3;">install</span></span>
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84
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> cd</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#8b9e8f1124050d1793c0beca78d203228ec949ca"><strong>c/src/alleleCounter.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** LICENSE</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#e48e40052652e64de8f1b45c47565b343b77ebcf"><strong>c/src/bam_access.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** LICENSE</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#55adaf5fef8455960a1f0d4a76bbd6d50c471267"><strong>c/src/bam_access.h</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** LICENSE</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#a155a9ca246a73bebef0c2f24aaa5caa21be38c2"><strong>c/tests/bam_access_tests.c</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** LICENSE</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#f65782c608e1cad8f0405797c356fc8016fa46d1"><strong>c/tests/minunit.h</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/** LICENSE</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">18 Genome Research Ltd. </span></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Copyright (c) 2014-20<span class="idiff left right">20 Genome Research Ltd.</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* This file is part of alleleCount.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* alleleCount is free software: you can redistribute it and/or modify it under<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* the terms of the GNU Affero General Public License as published by the Free<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Software Foundation; either version 3 of the License, or (at your option) any<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* later version.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* This program is distributed in the hope that it will be useful, but WITHOUT<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* details.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* You should have received a copy of the GNU Affero General Public License<span class="idiff left right"> </span></span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* along with this program. If not, see <http://www.gnu.org/licenses/>.<span class="idiff left right"> </span></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* This file is part of alleleCount.</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* alleleCount is free software: you can redistribute it and/or modify it under</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* the terms of the GNU Affero General Public License as published by the Free</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* Software Foundation; either version 3 of the License, or (at your option) any</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* later version.</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* This program is distributed in the hope that it will be useful, but WITHOUT</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* details.</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* You should have received a copy of the GNU Affero General Public License</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">* along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#undef NDEBUG</span></span>
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<li id="c4553b09bd8cb4bb87239a3d3bb9a84e38d9d7c2">
<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#c4553b09bd8cb4bb87239a3d3bb9a84e38d9d7c2"><strong>c/tests/runtests.sh</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="shell"><span class="c" style="color: #998; font-style: italic;">########## LICENSE ##########</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18 Genome Research Ltd. </span></span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20 Genome Research Ltd.</span></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This file is part of alleleCount.<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># alleleCount is free software: you can redistribute it and/or modify it under<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># the terms of the GNU Affero General Public License as published by the Free<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Software Foundation; either version 3 of the License, or (at your option) any<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># later version.<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful, but WITHOUT<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
16
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># details.<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># You should have received a copy of the GNU Affero General Public License<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># along with this program. If not, see <http://www.gnu.org/licenses/>.<span class="idiff left right"> </span></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This file is part of alleleCount.</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># alleleCount is free software: you can redistribute it and/or modify it under</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># the terms of the GNU Affero General Public License as published by the Free</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Software Foundation; either version 3 of the License, or (at your option) any</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># later version.</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful, but WITHOUT</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># details.</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># You should have received a copy of the GNU Affero General Public License</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###########################</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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22
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Running unit tests:"</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#31355477081907f59eb87bc628b4e3a7c370e451"><strong>perl/Makefile.PL</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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#4d78a438d73857820bc8ea5b4470a117b56e5f8a"><strong>perl/bin/alleleCounter.pl</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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#027f40d8d7bccd8caf08a7236885032f188780c1"><strong>perl/lib/Sanger/CGP/AlleleCount.pm</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Sanger::CGP::</span><span class="nv" style="color: #008080;">AlleleCount</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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>
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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">@@ -25,7 +25,7 @@ package Sanger::CGP::AlleleCount;</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">base</span> <span class="p">'</span><span class="s1" style="color: #d14;">Exporter</span><span class="p">';</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">4.2.<span class="idiff left right">0</span></span><span class="p">';</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">4.2.<span class="idiff left right">1</span></span><span class="p">';</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">@EXPORT</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qw($VERSION)</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="mi" style="color: #099;">1</span><span class="p">;</span></span></pre>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#d07b67fccf1ea50b9817db5a04f530385be5c808"><strong>perl/lib/Sanger/CGP/AlleleCount/Genotype.pm</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Sanger::CGP::AlleleCount::</span><span class="nv" style="color: #008080;">Genotype</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<li id="3aac7ffa1f2918a9dc1e8a379d762d892b207b9f">
<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#3aac7ffa1f2918a9dc1e8a379d762d892b207b9f"><strong>perl/t/1_pm_compile.t</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18 Genome Research Ltd. </span></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20 Genome Research Ltd.</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This file is part of alleleCount.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># alleleCount is free software: you can redistribute it and/or modify it under<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># the terms of the GNU Affero General Public License as published by the Free<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Software Foundation; either version 3 of the License, or (at your option) any<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># later version.<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful, but WITHOUT<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS<span class="idiff left right"> </span></span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more<span class="idiff left right"> </span></span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># details.<span class="idiff left right"> </span></span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU Affero General Public License<span class="idiff left right"> </span></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This file is part of alleleCount.</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># alleleCount is free software: you can redistribute it and/or modify it under</span></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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># the terms of the GNU Affero General Public License as published by the Free</span></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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Software Foundation; either version 3 of the License, or (at your option) any</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># later version.</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful, but WITHOUT</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more</span></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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># details.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU Affero General Public License</span></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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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"></span>
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<li id="060cf87839203496796c248124853fe18431aab7">
<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#060cf87839203496796c248124853fe18431aab7"><strong>perl/t/2_pl_compile.t</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="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18 Genome Research Ltd. </span></span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20 Genome Research Ltd.</span></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
6
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This file is part of alleleCount.<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
7
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
8
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># alleleCount is free software: you can redistribute it and/or modify it under<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># the terms of the GNU Affero General Public License as published by the Free<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
10
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Software Foundation; either version 3 of the License, or (at your option) any<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># later version.<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful, but WITHOUT<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS<span class="idiff left right"> </span></span></span>
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15
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more<span class="idiff left right"> </span></span></span>
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16
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># details.<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU Affero General Public License<span class="idiff left right"> </span></span></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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This file is part of alleleCount.</span></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="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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></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="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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># alleleCount is free software: you can redistribute it and/or modify it under</span></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="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">
9
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># the terms of the GNU Affero General Public License as published by the Free</span></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="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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Software Foundation; either version 3 of the License, or (at your option) any</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># later version.</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></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">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This program is distributed in the hope that it will be useful, but WITHOUT</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># details.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># You should have received a copy of the GNU Affero General Public License</span></span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"></span>
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<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#0253730b599615614b44f25db771a896d6f4809f"><strong>perl/t/genotype.t</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="perl"><span class="c1" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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5
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<td class="diff-line-num 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">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<li id="ce2209c3363c413f1acd1a7698a221ee5358c8ac">
<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#ce2209c3363c413f1acd1a7698a221ee5358c8ac"><strong>prerelease.sh</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="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<li id="592a1aae25926e838f4bca2e1c8981f30b077dda">
<a href="https://salsa.debian.org/med-team/allelecount/-/commit/77e90fde06749b7129ddaeb6853927d434708189#592a1aae25926e838f4bca2e1c8981f30b077dda"><strong>setup.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">18</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Copyright (c) 2014-20<span class="idiff left right">20</span> Genome Research Ltd.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: CASM/Cancer IT <cgphelp@sanger.ac.uk></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></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">@@ -21,52 +21,18 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##########LICENCE##########</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="nv" style="color: #008080;">SOURCE_HTSLIB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"https://github.com/samtools/htslib/releases/download/1.11/htslib-1.11.tar.bz2"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># ALL tool versions used by opt-build.sh</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># need to keep in sync with Dockerfile</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">VER_HTSLIB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"1.11"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">VER_LIBDEFLATE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"v1.6"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="nv" style="color: #008080;">EXP_SAMV</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"1.3.1"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell">version_gt <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">test</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">printf</span> <span class="s1" style="color: #d14;">'%s\n'</span> <span class="nv" style="color: #008080;">$@</span> | <span class="nb" style="color: #0086b3;">sort</span> <span class="nt" style="color: #000080;">-V</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n</span> 1<span class="si" style="color: #d14;">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell">get_distro <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"> <span class="nv" style="color: #008080;">EXT</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"> <span class="nv" style="color: #008080;">DECOMP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$2</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">*</span>.tar.bz2<span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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36
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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">EXT</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"tar.bz2"</span></span>
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37
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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"> <span class="nv" style="color: #008080;">DECOMP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-j"</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell"> <span class="k" style="font-weight: 600;">elif</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nv" style="color: #008080;">$2</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz<span class="k" style="font-weight: 600;">*</span> <span class="o" style="font-weight: 600;">]]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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39
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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">EXT</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"tar.gz"</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"> <span class="nv" style="color: #008080;">DECOMP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-z"</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"I don't understand the file type for </span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="shell"></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if </span><span class="nb" style="color: #0086b3;">hash </span>curl 2>/dev/null<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>curl <span class="nt" style="color: #000080;">-sS</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$1</span>.<span class="nv" style="color: #008080;">$EXT</span> <span class="nt" style="color: #000080;">-L</span> <span class="nv" style="color: #008080;">$2</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
49
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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>wget <span class="nt" style="color: #000080;">-nv</span> <span class="nt" style="color: #000080;">-O</span> <span class="nv" style="color: #008080;">$1</span>.<span class="nv" style="color: #008080;">$EXT</span> <span class="nv" style="color: #008080;">$2</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$1</span></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">--strip-components</span> 1 <span class="nt" style="color: #000080;">-C</span> <span class="nv" style="color: #008080;">$1</span> <span class="nv" style="color: #008080;">$DECOMP</span> <span class="nt" style="color: #000080;">-xf</span> <span class="nv" style="color: #008080;">$1</span>.<span class="nv" style="color: #008080;">$EXT</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="shell"></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="shell">get_file <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># output, source</span></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">hash </span>curl 2>/dev/null<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>curl <span class="nt" style="color: #000080;">-sS</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$1</span> <span class="nt" style="color: #000080;">-L</span> <span class="nv" style="color: #008080;">$2</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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60
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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>wget <span class="nt" style="color: #000080;">-nv</span> <span class="nt" style="color: #000080;">-O</span> <span class="nv" style="color: #008080;">$1</span> <span class="nv" style="color: #008080;">$2</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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63
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"></span>
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64
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="o" style="font-weight: 600;">(</span><span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-ne</span> 1 <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-ne</span> 2<span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">]]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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65
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please provide an installation path and optionally perl lib paths to allow, e.g."</span></span>
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66
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ./setup.sh /opt/myBundle"</span></span>
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67
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"OR all elements versioned:"</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ./setup.sh /opt/cgp<span class="idiff left right">Vcf-X.X.X /opt/PCAP</span>-X.X.X/lib/perl"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span><span class="idiff left right">0</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ./setup.sh /opt/cgp<span class="idiff left right">Pinel-X.X.X /opt/cgpVcf-X.X.X/lib/perl:/opt/PCAP-core</span>-X.X.X/lib/perl"</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span><span class="idiff left right">1</span></span>
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70
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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71
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"></span>
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72
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell"><span class="nv" style="color: #008080;">INST_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" 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="41" 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">@@ -75,17 +41,6 @@ if [[ $# -eq 2 ]] ; then</td>
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75
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">CGP_PERLLIBS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$2</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="shell"></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="shell"></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="shell"><span class="nv" style="color: #008080;">CPU</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-c</span> ^processor /proc/cpuinfo<span class="sb" style="color: #d14;">`</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CPU</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-gt</span> <span class="s2" style="color: #d14;">"6"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">CPU</span><span class="o" style="font-weight: 600;">=</span>6</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">CPU</span><span class="o" style="font-weight: 600;">=</span>1</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Max compilation CPUs set to </span><span class="nv" style="color: #008080;">$CPU</span><span class="s2" style="color: #d14;">"</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="shell"></span>
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89
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># get current directory</span></span>
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90
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nv" style="color: #008080;">INIT_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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91
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" 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="53" 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">@@ -98,7 +53,6 @@ INST_PATH=`pwd`</td>
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98
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$INIT_DIR</span></span>
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99
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># make sure that build is self contained</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>PERL5LIB</span>
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102
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"><span class="nv" style="color: #008080;">PERLROOT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span>/lib/perl5</span>
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103
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># allows user to knowingly specify other PERL5LIB areas.</span></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">@@ -108,91 +62,17 @@ else</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PERL5LIB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$PERLROOT</span><span class="s2" style="color: #d14;">:</span><span class="nv" style="color: #008080;">$CGP_PERLLIBS</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span>/bin:<span class="nv" style="color: #008080;">$PATH</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#create a location to build dependencies</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="shell"><span class="nv" style="color: #008080;">SETUP_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INIT_DIR</span>/install_tmp</span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## grab cpanm and stick in workspace, then do a self upgrade into bin:</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="shell">get_file <span class="nv" style="color: #008080;">$SETUP_DIR</span>/cpanm https://cpanmin.us/</span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="shell">perl <span class="nv" style="color: #008080;">$SETUP_DIR</span>/cpanm <span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$INST_PATH</span> App::cpanminus</span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="shell"><span class="nv" style="color: #008080;">CPANM</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>which cpanm<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/basePerlDeps.success <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Previously installed base perl deps..."</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">perlmods</span><span class="o" style="font-weight: 600;">=(</span> <span class="s2" style="color: #d14;">"ExtUtils::CBuilder"</span> <span class="s2" style="color: #d14;">"Module::Build~0.42"</span> <span class="s2" style="color: #d14;">"Const::Fast"</span> <span class="s2" style="color: #d14;">"File::Which"</span> <span class="s2" style="color: #d14;">"LWP::UserAgent"</span><span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">perlmods</span><span class="p">[@]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="shell"> <span class="nv" style="color: #008080;">$CPANM</span> <span class="nt" style="color: #000080;">--no-interactive</span> <span class="nt" style="color: #000080;">--notest</span> <span class="nt" style="color: #000080;">--mirror</span> http://cpan.metacpan.org <span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$INST_PATH</span> <span class="nv" style="color: #008080;">$i</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">touch</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/basePerlDeps.success</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="shell"></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="shell"></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/htslibGet.success <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" already staged ..."</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> cd</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span></span>
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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="shell"> get_distro <span class="s2" style="color: #d14;">"htslib"</span> <span class="nv" style="color: #008080;">$SOURCE_HTSLIB</span></span>
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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">touch</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/htslibGet.success</span>
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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"Building htslib ..."</span></span>
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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/htslib.success <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" previously installed ..."</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> mkdir</span> <span class="nt" style="color: #000080;">-p</span> htslib</span>
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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">--strip-components</span> 1 <span class="nt" style="color: #000080;">-C</span> htslib <span class="nt" style="color: #000080;">-jxf</span> htslib.tar.bz2</span>
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<td class="diff-line-num old old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd </span>htslib</span>
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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="shell"> ./configure <span class="nt" style="color: #000080;">--enable-plugins</span> <span class="nt" style="color: #000080;">--enable-libcurl</span> <span class="nt" style="color: #000080;">--prefix</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="shell"> make <span class="nt" style="color: #000080;">-j</span><span class="nv" style="color: #008080;">$CPU</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">touch</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/htslib.success</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="shell"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">HTSLIB</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SETUP_DIR</span><span class="s2" style="color: #d14;">/htslib"</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="shell"></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"Building alleleCounter ..."</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SETUP_DIR</span><span class="s2" style="color: #d14;">/alleleCounter.success"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" previously installed ..."</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$INIT_DIR</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$INIT_DIR</span>/c/bin</span>
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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="shell"> make <span class="nt" style="color: #000080;">-C</span> c clean</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="shell"> make <span class="nt" style="color: #000080;">-C</span> c <span class="nt" style="color: #000080;">-j</span><span class="nv" style="color: #008080;">$CPU</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cp</span> <span class="nv" style="color: #008080;">$INIT_DIR</span>/c/bin/alleleCounter <span class="nv" style="color: #008080;">$INST_PATH</span>/bin/.</span>
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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">touch</span> <span class="nv" style="color: #008080;">$SETUP_DIR</span>/alleleCounter.success</span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="shell"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$INIT_DIR</span>/perl</span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="shell"></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"Installing Perl prerequisites ..."</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">(</span> perl <span class="nt" style="color: #000080;">-MExtUtils</span>::MakeMaker <span class="nt" style="color: #000080;">-e</span> 1 <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1<span class="o" style="font-weight: 600;">)</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> echo</span> <span class="s2" style="color: #d14;">"WARNING: Your Perl installation does not seem to include a complete set of core modules. Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed. For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="shell"><span class="nv" style="color: #008080;">$CPANM</span> <span class="nt" style="color: #000080;">--no-interactive</span> <span class="nt" style="color: #000080;">--notest</span> <span class="nt" style="color: #000080;">--mirror</span> http://cpan.metacpan.org <span class="nt" style="color: #000080;">-l</span> <span class="nv" style="color: #008080;">$INST_PATH</span>/ <span class="nt" style="color: #000080;">--installdeps</span> <span class="nv" style="color: #008080;">$INIT_DIR</span>/perl/. < /dev/null</span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"Installing alleleCount ..."</span></span>
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<td class="diff-line-num old old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$INIT_DIR</span>/perl</span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="shell">perl Makefile.PL <span class="nv" style="color: #008080;">INSTALL_BASE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="shell">make</span>
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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="shell">make <span class="nb" style="color: #0086b3;">test</span></span>
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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="shell">make <span class="nb" style="color: #0086b3;">install</span></span>
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<td class="diff-line-num new old_line" data-linenumber="186" 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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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">OPT</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INST_PATH</span></span>
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<td class="diff-line-num old_line" data-linenumber="186" 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">
186
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># cleanup all junk</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="shell"><span class="nb" style="color: #0086b3;"><span class="idiff left">rm</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-rf</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$SETUP_DIR</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="idiff left">bash build/opt-build.sh </span><span class="nv" style="color: #008080;"><span class="idiff right">$INST_PATH</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="idiff left">bash build/opt-build-local.sh </span><span class="nv" style="color: #008080;"><span class="idiff right">$INST_PATH</span></span></span>
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189
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<td class="diff-line-num new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell"></span>
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190
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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191
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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192
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<td class="diff-line-num new_line old" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please add the following to beginning of <span class="idiff left right">path</span>:"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="193" 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="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please add the following to beginning of <span class="idiff left right">PATH</span>:"</span></span>
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<td class="diff-line-num old_line" data-linenumber="193" 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">
193
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<td class="diff-line-num new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" </span><span class="nv" style="color: #008080;">$INST_PATH</span><span class="s2" style="color: #d14;">/bin"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
194
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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please add the following to beginning of <span class="idiff left right">PERL5LIB</span>:"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" </span><span class="nv" style="color: #008080;">$<span class="idiff left right">PERLROOT</span></span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please add the following to beginning of <span class="idiff left right">LD_LIBRARY_PATH</span>:"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" </span><span class="nv" style="color: #008080;">$<span class="idiff left">INST_PATH</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/lib</span>"</span></span>
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<td class="diff-line-num old_line" data-linenumber="196" 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">
196
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<td class="diff-line-num new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num old_line" data-linenumber="197" 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">
197
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<td class="diff-line-num new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="198" 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">
198
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exit </span>0</span></pre>
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