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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pirs">Debian Med / pirs</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pirs/-/commit/69fa5d010a4a19f04832fb61c3b7ef549ff72bd3">69fa5d01</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-08-31T15:58:41+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pirs/-/commit/e2ce3eeddc9a7a1e9f34cf89f0ebbe3f0efc03ec">e2ce3eed</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-08-31T15:59:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pirs/-/commit/ec9ca2aaf8682ccb08c0d096a52f1a1558340b53">ec9ca2aa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-08-31T15:59:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Apply multi-arch hints.
+ pirs-examples, pirs-profiles: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pirs/-/commit/63c63cdbf39c9d5a82de53344ab4cef4a2b40420">63c63cdb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-08-31T16:15:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use default name run-unit-test for autopkgtest script
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pirs/-/commit/44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f">44f20b4c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-08-31T16:17:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#4ecf6df0b8f4a59fb1bb73e697d93b0d8e2f5503">
debian/pirs.docs
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#7a704765362822e0a930cac063819da76c62a460">
<span class="deleted-file">
−
debian/tests/gcContCvgBias-test
</span>
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/pirs-test
→
debian/tests/run-unit-test
</a>
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">Notes</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">how</span> <span class="n" style="color: #333;">this</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span><span class="mf" style="color: #099;">.</span></span>
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<td class="new_line diff-line-num new" 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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<td class="new_line diff-line-num new" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" 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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nc" style="color: #458; font-weight: 600;">This</span> <span class="n" style="color: #333;">package</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">tested</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">provided</span> <span class="n" style="color: #333;">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="new_line diff-line-num new" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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<td class="new_line diff-line-num new" 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="php"> <span class="n" style="color: #333;">sudo</span> <span class="n" style="color: #333;">apt</span> <span class="n" style="color: #333;">install</span> <span class="n" style="color: #333;">pirs</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">examples</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="php"> <span class="n" style="color: #333;">sh</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">unit</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">test</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="n" style="color: #333;">in</span> <span class="n" style="color: #333;">order</span> <span class="n" style="color: #333;">to</span> <span class="n" style="color: #333;">confirm</span> <span class="n" style="color: #333;">its</span> <span class="n" style="color: #333;">integrity</span><span class="mf" style="color: #099;">.</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pirs (2.0.2+dfsg-10) unstable; 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"> * Fix watchfile to detect new versions on github (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Apply multi-arch hints.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> + pirs-examples, pirs-profiles: Add Multi-Arch: foreign.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Use default name run-unit-test for autopkgtest script</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 31 Aug 2021 16:15:12 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">pirs (2.0.2+dfsg-9) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> libboost-dev,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libgzstream-dev</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pirs</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pirs.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://github.com/galaxy001/pirs</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" 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">@@ -42,6 +42,7 @@ Description: Profile based Illumina pair-end Reads Simulator</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">Package: pirs-profiles</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Description: profile basd Illumina pair-end Reads Simulator (profile data)</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> The program pIRS can be used for simulating Illumina PE reads, with a</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> series of characters generated by Illumina sequencing platform, such as</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="67" 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">@@ -66,6 +67,7 @@ Description: profile basd Illumina pair-end Reads Simulator (profile data)</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">Package: pirs-examples</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">Description: profile basd Illumina pair-end Reads Simulator (example data)</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> The program pIRS can be used for simulating Illumina PE reads, with a</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"> series of characters generated by Illumina sequencing platform, such as</span>
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<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#4ecf6df0b8f4a59fb1bb73e697d93b0d8e2f5503"><strong>debian/pirs.docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/README.test</span></pre>
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<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: <span class="idiff left right">gcContCvgBias-test, pirs</span>-test</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: <span class="idiff left right">run-unit</span>-test</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: @, pirs-examples</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#7a704765362822e0a930cac063819da76c62a460"><strong>debian/tests/gcContCvgBias-test</strong>
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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>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>pirs</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">testbin</span><span class="o" style="font-weight: 600;">=</span>gcContCvgBias</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC6" 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;">$AUTOPKGTEST_TMP</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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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">testbin</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC13" 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;">testbin</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># find . -type f -name "*.gz" -exec gunzip \{\} \;</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell">gc_coverage_bias <span class="nt" style="color: #000080;">-r</span> gcdeptestref.fa.gz <span class="nt" style="color: #000080;">-o</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-w</span> 100,200 <span class="nt" style="color: #000080;">--gcdump</span> <span class="nt" style="color: #000080;">--depwindump</span> gcdeptest.depth.gz</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">gc_coverage_bias_plot test_100.dat</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">gc_coverage_bias_plot test_200.dat</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-l</span> <span class="nb" style="color: #0086b3;">test</span><span class="k" style="font-weight: 600;">*</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/pirs-test</strong>
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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>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>pirs</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">testbin</span><span class="o" style="font-weight: 600;">=</span>pirs</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" 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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">testbin</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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12
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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;">${</span><span class="nv" style="color: #008080;">testbin</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir </span>gcContCvgBias</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>gcContCvgBias</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/gcContCvgBias/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</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;"># find . -type f -name "*.gz" -exec gunzip \{\} \;</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">gc_coverage_bias <span class="nt" style="color: #000080;">-r</span> gcdeptestref.fa.gz <span class="nt" style="color: #000080;">-o</span> <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-w</span> 100,200 <span class="nt" style="color: #000080;">--gcdump</span> <span class="nt" style="color: #000080;">--depwindump</span> gcdeptest.depth.gz</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">gc_coverage_bias_plot test_100.dat</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">gc_coverage_bias_plot test_200.dat</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-l</span> <span class="nb" style="color: #0086b3;">test</span><span class="k" style="font-weight: 600;">*</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir </span>pirs</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>pirs</span>
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<pre style="margin: 0;">+<span id="LC25" 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/pirs/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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14
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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15
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"></span>
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16
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell">pirs diploid ref_seq.fa <span class="nt" style="color: #000080;">-s</span> 0.001 <span class="nt" style="color: #000080;">-R</span> 2 <span class="nt" style="color: #000080;">-d</span> 0.0001 <span class="nt" style="color: #000080;">-v</span> 0.000001 <span class="nt" style="color: #000080;">-c</span> <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: #000080;">-o</span> ref22 <span class="o" style="font-weight: 600;">></span>SimDiploid.out 2>SimDiploid.err</span>
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<a href="https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</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="plaintext">version=4</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="plaintext"></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="plaintext">opts="uversionmangle=s/b/~b/;s/(\d)(\d+)/$1.$2/,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/galaxy001/pirs/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/galaxy001/pirs/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></pre>
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