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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/drop-seq">Debian Med / drop-seq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/5df8913ec4e8596f29897cf2d68f661c111f4ef8">5df8913e</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T15:20:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Link to excluded file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/bcb673f29930cc1f5d2df442931dc33c32f4570a">bcb673f2</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T20:36:35+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install scripts that come with this package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/8f3db984b1ac499b00cd13530a225161cc42c5b8">8f3db984</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T20:37:01+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install reference data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/drop-seq/-/commit/b85b04a2cf27ed28d35c8f821eedae08d85fd20d">b85b04a2</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T20:37:15+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/drop-seq/-/commit/7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7">7203c8e0</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T20:40:43+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
</li>
</ul>
<h4>15 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="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
debian/docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#7ffb40db84d44a3aa259423c43d23bbbcd64bff7">
debian/drop-seq-testdata.install
</a>
</li>
<li class="file-stats">
<a href="#fa3c4511b712375e46ccf910634c0c155877d888">
debian/drop-seq-tools.install
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<li class="file-stats">
<a href="#a2a0f2265fe4fea07d13f31356bde869bdcd56fd">
<span class="new-file">
+
debian/patches/link_excluded_file.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#23109b43316c249f906a977d1143e31dcdbc442b">
<span class="new-file">
+
debian/tests/ref/FilterBam.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#1c3e3d1132dfe3686c9216308bbd12e5df2d21c2">
<span class="new-file">
+
debian/tests/ref/PolyATrimmer.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#d5d5d2b3b8004f721a50234f5f1976ee8af9514d">
<span class="new-file">
+
debian/tests/ref/README.test_data
</span>
</a>
</li>
<li class="file-stats">
<a href="#7c92670d131d242a3916b6735a1e592fbd4ed61a">
<span class="new-file">
+
debian/tests/ref/TagBamWithReadSequenceExtended-cellular.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#b091b0568f53c6e61a3ff198cc59fcaaf28dc5ea">
<span class="new-file">
+
debian/tests/ref/TagBamWithReadSequenceExtended-molecular.sam
</span>
</a>
</li>
<li class="file-stats">
<a href="#83522fd991d396a7f4ac026d37ae653cfbd62884">
<span class="new-file">
+
debian/tests/ref/TrimStartingSequence.sam
</span>
</a>
</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/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#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>
</pre>
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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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<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="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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<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="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/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">drop-seq (2.3.0+dfsg-3) UNRELEASED; urgency=medium</span>
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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"> * Link to excluded file</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 scripts that come with this package</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Install reference data</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add autopkgtests</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"> * Install docs</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"> -- Pranav Ballaney <ballaneypranav@gmail.com> Tue, 16 Jun 2020 20:37:20 +0530</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">drop-seq (2.3.0+dfsg-2) 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"> * debhelper-compat 13 (routine-update)</span>
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<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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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>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/ref/README*</span></pre>
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<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#7ffb40db84d44a3aa259423c43d23bbbcd64bff7"><strong>debian/drop-seq-testdata.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="nx">testdata</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">drop</span><span class="o" style="font-weight: 600;">-</span><span class="nx">seq</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">testdata</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">drop</span><span class="o" style="font-weight: 600;">-</span><span class="nx">seq</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ref</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">drop</span><span class="o" style="font-weight: 600;">-</span><span class="nx">seq</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#fa3c4511b712375e46ccf910634c0c155877d888"><strong>debian/drop-seq-tools.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span> <span class="nx">usr</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">src</span><span class="o" style="font-weight: 600;">/</span><span class="nx">scripts</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#a2a0f2265fe4fea07d13f31356bde869bdcd56fd"><strong>debian/patches/link_excluded_file.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -6,4 +6,4 @@</span> You may also use this address to be adde</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> See https://github.com/broadinstitute/Drop-seq/releases to download binaries.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-See [Drop-seq alignment cookbook](doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</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">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+See [Drop-seq alignment cookbook](https://github.com/broadinstitute/Drop-seq/blob/master/doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">no_git.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian_packaged_libs.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">link_excluded_file.patch</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#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: @, samtools</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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<li id="23109b43316c249f906a977d1143e31dcdbc442b">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#23109b43316c249f906a977d1143e31dcdbc442b"><strong>debian/tests/ref/FilterBam.sam</strong></a>
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<li id="1c3e3d1132dfe3686c9216308bbd12e5df2d21c2">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#1c3e3d1132dfe3686c9216308bbd12e5df2d21c2"><strong>debian/tests/ref/PolyATrimmer.sam</strong></a>
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</li>
<li id="d5d5d2b3b8004f721a50234f5f1976ee8af9514d">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#d5d5d2b3b8004f721a50234f5f1976ee8af9514d"><strong>debian/tests/ref/README.test_data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">The files used as references for testing were obtained by running the software on</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">the data provided in the testdata folder with this package.</span></pre>
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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">\ No newline at end of file</td>
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<li id="7c92670d131d242a3916b6735a1e592fbd4ed61a">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#7c92670d131d242a3916b6735a1e592fbd4ed61a"><strong>debian/tests/ref/TagBamWithReadSequenceExtended-cellular.sam</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">000000000-AMY9M:1:1111:13708:20052 0 1 565193 3 24M * 0 0 GTATTTCCTCACGCAAGCAACCGC BBBBBFDFFFFAGG?EGGGGCFEC XC:Z:GTATTTCCTCAC MD:Z:24 XF:Z:INTERGENIC PG:Z:STAR RG:Z:00000.1 XG:Z:RP5-857K21.4 NH:i:2 NM:i:0 XM:Z:CTAATATG ZP:i:25 UQ:i:0 AS:i:23 gf:Z:INTRONIC gn:Z:RP5-857K21.4 gs:Z:-</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">000000000-AMY9M:1:2104:20987:12124 16 1 6246604 1 50M * 0 0 GGAAGCCCTTTGACTATGATTTCCAATTTTCTGTTCAATCCACACTGCAG HHGCFAHFGDHGGHHGHGHHHHGGHHHHFGGGGGGFGGBBFFFFF3BBBA XC:Z:GGAAGCCCTTTG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:RPL22 NH:i:3 NM:i:0 XM:Z:GTTGGGCC UQ:i:0 AS:i:49 gf:Z:CODING,UTR gn:Z:RPL22,RPL22 gs:Z:-,-</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">000000000-AMY9M:1:1114:17300:12082 0 1 16058910 255 50M * 0 0 CCTCTTTACGTGCCATGAGGATTGCCAGACCAGCTTCTTCCGCTCTTTGG BBBBBFFFFACFFGGGGGCGGFDGGHH4GGHHFHHFHHHHHDG2EHFGG3 XC:Z:CCTCTTTACGTG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:AAGACCAC UQ:i:0 AS:i:49 gf:Z:CODING,CODING gn:Z:PLEKHM2,RP11-288I21.1 gs:Z:+,-</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">000000000-AMY9M:1:2104:15433:7166 0 1 16059019 255 6M82N44M * 0 0 GTCTTGGAGTTCTCCCAGGACAGCCAGCAGCTCCTCCCGCCCTGGGTCAT AAABBFFFBCCFGGGGGGCGGGAGHHHGHHHHHGHHHGGGGGGHHAGGAG XC:Z:GTCTTGGAGTTC MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:AAGACCAC UQ:i:0 AS:i:50 gf:Z:CODING,CODING,INTRONIC gn:Z:PLEKHM2,RP11-288I21.1,RP11-288I21.1 gs:Z:+,-,-</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">000000000-AMY9M:1:2109:19958:23569 0 1 38484134 255 12S38M * 0 0 GGGTTAAACTCCAGGCTGGAGTACATATTATTAAGGAGACTAAGGAAGAA ?AAAAA1DFFFFF1C1AAE1GGGHHHBGB33GAE1G1BGEBGFHGGB0GH XC:Z:GGGTTAAACTCC MD:Z:3A34 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:UTP11L NH:i:1 NM:i:1 XM:Z:GGGAGTCG UQ:i:16 AS:i:35 gf:Z:CODING,INTRONIC gn:Z:UTP11L,UTP11L gs:Z:+,+</span></pre>
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<li id="b091b0568f53c6e61a3ff198cc59fcaaf28dc5ea">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#b091b0568f53c6e61a3ff198cc59fcaaf28dc5ea"><strong>debian/tests/ref/TagBamWithReadSequenceExtended-molecular.sam</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">000000000-AMY9M:1:1111:13708:20052 0 1 565193 3 24M * 0 0 GTATTTCCTCACGCAAGCAACCGC BBBBBFDFFFFAGG?EGGGGCFEC XC:Z:CGCCTCCTCCGA MD:Z:24 XF:Z:INTERGENIC PG:Z:STAR RG:Z:00000.1 XG:Z:RP5-857K21.4 NH:i:2 NM:i:0 XM:Z:GTATTTCCTCAC ZP:i:25 UQ:i:0 AS:i:23 gf:Z:INTRONIC gn:Z:RP5-857K21.4 gs:Z:-</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">000000000-AMY9M:1:2104:20987:12124 16 1 6246604 1 50M * 0 0 GGAAGCCCTTTGACTATGATTTCCAATTTTCTGTTCAATCCACACTGCAG HHGCFAHFGDHGGHHGHGHHHHGGHHHHFGGGGGGFGGBBFFFFF3BBBA XC:Z:TGGCTGTTCTTT MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:RPL22 NH:i:3 NM:i:0 XM:Z:GGAAGCCCTTTG UQ:i:0 AS:i:49 gf:Z:CODING,UTR gn:Z:RPL22,RPL22 gs:Z:-,-</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">000000000-AMY9M:1:1114:17300:12082 0 1 16058910 255 50M * 0 0 CCTCTTTACGTGCCATGAGGATTGCCAGACCAGCTTCTTCCGCTCTTTGG BBBBBFFFFACFFGGGGGCGGFDGGHH4GGHHFHHFHHHHHDG2EHFGG3 XC:Z:AGTGAGACAAGG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:CCTCTTTACGTG UQ:i:0 AS:i:49 gf:Z:CODING,CODING gn:Z:PLEKHM2,RP11-288I21.1 gs:Z:+,-</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">000000000-AMY9M:1:2104:15433:7166 0 1 16059019 255 6M82N44M * 0 0 GTCTTGGAGTTCTCCCAGGACAGCCAGCAGCTCCTCCCGCCCTGGGTCAT AAABBFFFBCCFGGGGGGCGGGAGHHHGHHHHHGHHHGGGGGGHHAGGAG XC:Z:AGTGAGACAAGG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:GTCTTGGAGTTC UQ:i:0 AS:i:50 gf:Z:CODING,CODING,INTRONIC gn:Z:PLEKHM2,RP11-288I21.1,RP11-288I21.1 gs:Z:+,-,-</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">000000000-AMY9M:1:2109:19958:23569 0 1 38484134 255 12S38M * 0 0 GGGTTAAACTCCAGGCTGGAGTACATATTATTAAGGAGACTAAGGAAGAA ?AAAAA1DFFFFF1C1AAE1GGGHHHBGB33GAE1G1BGEBGFHGGB0GH XC:Z:AGTGAGACAAGG MD:Z:3A34 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:UTP11L NH:i:1 NM:i:1 XM:Z:GGGTTAAACTCC UQ:i:16 AS:i:35 gf:Z:CODING,INTRONIC gn:Z:UTP11L,UTP11L gs:Z:+,+</span></pre>
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<li id="83522fd991d396a7f4ac026d37ae653cfbd62884">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#83522fd991d396a7f4ac026d37ae653cfbd62884"><strong>debian/tests/ref/TrimStartingSequence.sam</strong></a>
The diff for this file was not included because it is too large.
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7#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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2
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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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3
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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>drop-seq</span>
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5
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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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7
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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<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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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC15" 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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" 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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># gunzip -r mm10/*</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> ref/<span class="k" style="font-weight: 600;">*</span></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;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> org/broadinstitute/dropseq/annotation/<span class="k" style="font-weight: 600;">*</span></span>
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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;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> org/broadinstitute/dropseq/readtrimming/<span class="k" style="font-weight: 600;">*</span></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>out</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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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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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="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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">drop-seq TagBamWithReadSequenceExtended <span class="nv" style="color: #008080;">INPUT</span><span class="o" style="font-weight: 600;">=</span>org/broadinstitute/dropseq/annotation/test.bam <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"> <span class="nv" style="color: #008080;">OUTPUT</span><span class="o" style="font-weight: 600;">=</span>out/TagBamWithReadSequenceExtended-cellular.bam <span class="nv" style="color: #008080;">SUMMARY</span><span class="o" style="font-weight: 600;">=</span>TagBamWithReadSequenceExtended-cellular.bam_summary.txt <span class="nv" style="color: #008080;">BASE_RANGE</span><span class="o" style="font-weight: 600;">=</span>1-12 <span class="nv" style="color: #008080;">BASE_QUALITY</span><span class="o" style="font-weight: 600;">=</span>10 <span class="nv" style="color: #008080;">BARCODED_READ</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">DISCARD_READ</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false </span><span class="nv" style="color: #008080;">TAG_NAME</span><span class="o" style="font-weight: 600;">=</span>XC <span class="nv" style="color: #008080;">NUM_BASES_BELOW_QUALITY</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">samtools view out/TagBamWithReadSequenceExtended-cellular.bam <span class="o" style="font-weight: 600;">></span> out/TagBamWithReadSequenceExtended-cellular.sam</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">diff out/TagBamWithReadSequenceExtended-cellular.sam ref/TagBamWithReadSequenceExtended-cellular.sam</span>
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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>
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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>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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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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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">drop-seq TagBamWithReadSequenceExtended <span class="nv" style="color: #008080;">INPUT</span><span class="o" style="font-weight: 600;">=</span>org/broadinstitute/dropseq/annotation/test.bam <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nv" style="color: #008080;">OUTPUT</span><span class="o" style="font-weight: 600;">=</span>out/TagBamWithReadSequenceExtended-molecular.bam <span class="nv" style="color: #008080;">SUMMARY</span><span class="o" style="font-weight: 600;">=</span>TagBamWithReadSequenceExtended-molecular.bam_summary.txt <span class="nv" style="color: #008080;">BASE_RANGE</span><span class="o" style="font-weight: 600;">=</span>1-12 <span class="nv" style="color: #008080;">BASE_QUALITY</span><span class="o" style="font-weight: 600;">=</span>10 <span class="nv" style="color: #008080;">BARCODED_READ</span><span class="o" style="font-weight: 600;">=</span>1 <span class="nv" style="color: #008080;">DISCARD_READ</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false </span><span class="nv" style="color: #008080;">TAG_NAME</span><span class="o" style="font-weight: 600;">=</span>XM <span class="nv" style="color: #008080;">NUM_BASES_BELOW_QUALITY</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">samtools view out/TagBamWithReadSequenceExtended-molecular.bam <span class="o" style="font-weight: 600;">></span> out/TagBamWithReadSequenceExtended-molecular.sam</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">diff out/TagBamWithReadSequenceExtended-molecular.sam ref/TagBamWithReadSequenceExtended-molecular.sam</span>
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39
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<pre style="margin: 0;">+<span id="LC39" 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>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" 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 3</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">drop-seq FilterBam <span class="nv" style="color: #008080;">TAG_REJECT</span><span class="o" style="font-weight: 600;">=</span>XQ <span class="nv" style="color: #008080;">INPUT</span><span class="o" style="font-weight: 600;">=</span>org/broadinstitute/dropseq/readtrimming/N701.subset.tagged_filtered.sam <span class="se" style="color: #d14;">\</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nv" style="color: #008080;">OUTPUT</span><span class="o" style="font-weight: 600;">=</span>out/FilterBam.bam</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell">samtools view out/FilterBam.bam <span class="o" style="font-weight: 600;">></span> out/FilterBam.sam</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell">diff out/FilterBam.sam ref/FilterBam.sam</span>
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47
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<pre style="margin: 0;">+<span id="LC47" 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>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" 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 4</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell">drop-seq TrimStartingSequence <span class="nv" style="color: #008080;">INPUT</span><span class="o" style="font-weight: 600;">=</span>out/FilterBam.bam <span class="nv" style="color: #008080;">OUTPUT</span><span class="o" style="font-weight: 600;">=</span>out/TrimStartingSequence.bam <span class="se" style="color: #d14;">\</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"> <span class="nv" style="color: #008080;">OUTPUT_SUMMARY</span><span class="o" style="font-weight: 600;">=</span>out/TrimStartingSequence.summary.txt <span class="nv" style="color: #008080;">SEQUENCE</span><span class="o" style="font-weight: 600;">=</span>AAGCAGTGGTATCAACGCAGAGTGAATGGG <span class="nv" style="color: #008080;">MISMATCHES</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nv" style="color: #008080;">NUM_BASES</span><span class="o" style="font-weight: 600;">=</span>5</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell">samtools view out/TrimStartingSequence.bam <span class="o" style="font-weight: 600;">></span> out/TrimStartingSequence.sam</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell">diff out/TrimStartingSequence.sam ref/TrimStartingSequence.sam</span>
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55
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<pre style="margin: 0;">+<span id="LC55" 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>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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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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58
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<pre style="margin: 0;">+<span id="LC58" 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 5</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell">drop-seq PolyATrimmer <span class="nv" style="color: #008080;">INPUT</span><span class="o" style="font-weight: 600;">=</span>out/TrimStartingSequence.bam <span class="nv" style="color: #008080;">OUTPUT</span><span class="o" style="font-weight: 600;">=</span>out/PolyATrimmer.bam <span class="se" style="color: #d14;">\</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"> <span class="nv" style="color: #008080;">OUTPUT_SUMMARY</span><span class="o" style="font-weight: 600;">=</span>out/PolyATrimmer.summary.bam <span class="nv" style="color: #008080;">MISMATCHES</span><span class="o" style="font-weight: 600;">=</span>0 <span class="nv" style="color: #008080;">NUM_BASES</span><span class="o" style="font-weight: 600;">=</span>6 <span class="nv" style="color: #008080;">USE_NEW_TRIMMER</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell">samtools view out/PolyATrimmer.bam <span class="o" style="font-weight: 600;">></span> out/PolyATrimmer.sam</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell">diff out/PolyATrimmer.sam ref/PolyATrimmer.sam</span>
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63
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<pre style="margin: 0;">+<span id="LC63" 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>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"></span></pre>
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