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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/commit/d3135f776e02eccc42d72636531bcd18c5c9a1c4">d3135f77</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2019-09-19T19:03:03Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/tests/ to use wrapper
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<strong><a href="https://salsa.debian.org/med-team/beagle/commit/ed81b24f9962f9c6937a023b2f16ad4bb816ab57">ed81b24f</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2019-09-19T19:19:16Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>2 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#5cc37fd93ea78de7fa21d0db40d2e809ed627fc3">
debian/tests/run-sample-analysis
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/beagle/compare/a5f00fabec95a94c987ed178b52912cb9717827a...ed81b24f9962f9c6937a023b2f16ad4bb816ab57#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">beagle (5.1-190824+dfsg-2) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">beagle (5.1-190824+dfsg-2) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<li id="5cc37fd93ea78de7fa21d0db40d2e809ed627fc3">
<a href="https://salsa.debian.org/med-team/beagle/compare/a5f00fabec95a94c987ed178b52912cb9717827a...ed81b24f9962f9c6937a023b2f16ad4bb816ab57#5cc37fd93ea78de7fa21d0db40d2e809ed627fc3"><strong>debian/tests/run-sample-analysis</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/sh -e</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># http://dep.debian.net/deps/dep8/</span></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;"># Autopkgtest: Test if beagle run analysis correctly</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;"># Author: Dylan Aïssi <<span class="idiff left right">bob.dybian@gmail.com</span>></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;"># Last-Update: 201<span class="idiff left right">8-09-16</span></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;"># Author: Dylan Aïssi <<span class="idiff left right">daissi@debian.org</span>></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;"># Last-Update: 201<span class="idiff left right">9-09-19</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>beagle</span>
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<pre style="margin: 0;"> <span id="LC8" 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;">$ADTTMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,21 +11,19 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$ADTTMP</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$ADTTMP</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nv" style="color: #008080;">BEAGLE_TEST</span><span class="o" style="font-weight: 600;">=</span><span class="s1" style="color: #d14;">'java -jar /usr/share/beagle/beagle.jar'</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generate necessary files</span></span>
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17
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gzip </span>test.vcf</span>
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18
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell">zcat test.vcf.gz | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1-190</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s1" style="color: #d14;">'/'</span> <span class="s1" style="color: #d14;">'|'</span> | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> ref.vcf.gz</span>
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19
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell">zcat test.vcf.gz | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1-9</span>,191-200 | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> target.vcf.gz</span>
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20
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="idiff left">java </span><span class="nt" style="color: #000080;"><span class="idiff">-jar</span></span><span class="idiff right"> /usr/share/beagle/bref3.jar</span> ref.vcf.gz <span class="o" style="font-weight: 600;">></span> ref.bref3</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="idiff left right">bref3</span> ref.vcf.gz <span class="o" style="font-weight: 600;">></span> ref.bref3</span>
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21
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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22
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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;"># Beagle with gt argument</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;"><span class="idiff left right">$BEAGLE_TEST</span></span> <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>test.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.gt</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="idiff left right">beagle</span> <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>test.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.gt</span>
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24
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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25
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Beagle with ref and gt argument</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="nv" style="color: #008080;"><span class="idiff left right">$BEAGLE_TEST</span></span> <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">=</span>ref.vcf.gz <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>target.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.ref</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="idiff left right">beagle</span> <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">=</span>ref.vcf.gz <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>target.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.ref</span>
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27
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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28
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Beagle with bref3 file</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;"><span class="idiff left right">$BEAGLE_TEST</span></span> <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">=</span>ref.bref3 <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>target.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.bref3</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="idiff left right">beagle</span> <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">=</span>ref.bref3 <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>target.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.bref3</span>
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30
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$ADTTMP</span>/<span class="k" style="font-weight: 600;">*</span></span></pre>
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