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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/pbdagcon">Debian Med / pbdagcon</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/9edbe803052d3ed2d627b7a3173dd4bca413ac59">9edbe803</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:02:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/e1512cb458cb9806d35020cec606f954cc77fabf">e1512cb4</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:03:04+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/46d56dc78add36cd1f3472eaec4a2a824750a05e">46d56dc7</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:03:36+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add Pranav Ballaney to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/034d930ed3b380869796cd9ffc49073b8249fbf7">034d930e</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:03:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/30a4838d13a1d189da87bee5669b715c93e948a7">30a4838d</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:04:10+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/fed1eef638577ee5e910a3a41c22b1e50d496d9f">fed1eef6</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:04:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/e4f04611ccd288a8d48f507f6c11b1af10474a18">e4f04611</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:04:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pbdagcon/-/commit/4507c237ca1676a0acb8e6e95925a9b4340518ca">4507c237</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-08-24T01:05:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>7 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
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</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">
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></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="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></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="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></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="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pbdagcon (0.3+git20180411.c14c422+dfsg-2) unstable; urgency=medium</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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></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="plaintext"> * Add autopkgtests</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="plaintext"> * Install docs</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add Pranav Ballaney to Uploaders</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="plaintext"> * debhelper-compat 13 (routine-update)</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="plaintext"> * Add salsa-ci file (routine-update)</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="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Mon, 24 Aug 2020 01:04:20 +0530</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">pbdagcon (0.3+git20180411.c14c422+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Add myself to Uploaders to have at least one human uploader after</span>
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<a href="https://salsa.debian.org/med-team/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: pbdagcon</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Pranav Ballaney <ballaneypranav@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libhdf5-dev,</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,6 +20,7 @@ Standards-Version: 4.5.0</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pbdagcon</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pbdagcon.git</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/pbdagcon</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Package: pbdagcon</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</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/pbdagcon/-/compare/34e42f3da102b3840ce3876056d6d8fb119c6d6b...4507c237ca1676a0acb8e6e95925a9b4340518ca#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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 class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>pbdagcon</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="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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<pre style="margin: 0;">+<span id="LC7" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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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;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 1</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</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="shell">rangen 0.005 <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span> target.fasta</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">fasta2DAM target target.fasta</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">dsimulator target <span class="nt" style="color: #000080;">-c20</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span> queries.fasta</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">blasr queries.fasta target.fasta <span class="nt" style="color: #000080;">-m</span> 5 <span class="nt" style="color: #000080;">--out</span> mapped.m5</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">pbdagcon mapped.m5 <span class="o" style="font-weight: 600;">></span> consensus.fasta</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></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;">echo</span> <span class="s2" style="color: #d14;">"6977ed74eab5a8b58c3a90e10f1cb96c consensus.fasta"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"327a35213054ec8702ea35b85f3b3c44 mapped.m5"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"11015d691ec4d33c7ec4d8125349b739 queries.fasta"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"160c2f8c3aeb52c98403c2c1c677c13e target.dam"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"63690c9bbfd08ef3ff51d040d619056a target.fasta"</span> <span class="o" style="font-weight: 600;">>></span> checksums</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">md5sum</span> <span class="nt" style="color: #000080;">--check</span> checksums</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
</pre>
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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="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[93m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mTest 2</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">rangen 0.01 <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span>R.fasta </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">fasta2DAM R R.fasta </span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">dsimulator R <span class="nt" style="color: #000080;">-c20</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span>G.fasta </span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">fasta2DB G G.fasta </span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">DBsplit <span class="nt" style="color: #000080;">-s0</span>.1 G </span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">DBdust G.1 </span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">DBdust G.2 </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell">HPC.daligner <span class="nt" style="color: #000080;">-mdust</span> <span class="nt" style="color: #000080;">-t5</span> G | sh <span class="nt" style="color: #000080;">-v</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">dazcon <span class="nt" style="color: #000080;">-ox</span> <span class="nt" style="color: #000080;">-j</span> 4 <span class="nt" style="color: #000080;">-s</span> G.db <span class="nt" style="color: #000080;">-a</span> G.1.las <span class="o" style="font-weight: 600;">></span> corrected.fasta</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span></pre>
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