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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/ivar">Debian Med / ivar</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/06ee9d1c37759a205194b90d2ca1de992a2d29d2">06ee9d1c</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T21:52:59+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add reference data for autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/faee74402729006468baf6d98efc6ddc4a8f2e65">faee7440</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T21:53:14+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add recommended package as per docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/a2f912c4dd9b97eef9c6c2dc46605caeba245f84">a2f912c4</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T21:53:47+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/ivar/-/commit/355391c7b2a4ca9f268d146488cc2e64111eb241">355391c7</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-06-16T21:56:26+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs and examples
</pre>
</li>
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<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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debian/README.test
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
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debian/examples
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<li class="file-stats">
<a href="#74a6f0227a087e1ff878da7036efea2a91d873c4">
debian/ivar.docs
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<li class="file-stats">
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debian/tests/control
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debian/tests/ref/README.test_data
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debian/tests/ref/out-consensus.fa
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debian/tests/ref/out-consensus.qual.txt
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debian/tests/ref/out-filtered.tsv
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debian/tests/ref/out-getmasked.txt
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debian/tests/ref/out-removereads.sam
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debian/tests/ref/out-trim.sam
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debian/tests/ref/out-trim2.sam
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debian/tests/ref/out-variants.tsv
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#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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<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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<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/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ivar (1.2.2+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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add reference data for autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add recommended package as per docs</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Install docs and examples</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Tue, 16 Jun 2020 21:55:42 +0530</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">ivar (1.2.2+dfsg-2) unstable; urgency=medium</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"> * debhelper-compat 13 (routine-update)</span>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#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">@@ -15,6 +15,7 @@ Package: ivar</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Recommends: samtools</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Description: functions broadly useful for viral amplicon-based sequencing</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> iVar is a computational package that contains functions broadly useful</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> for viral amplicon-based sequencing. Additional tools for metagenomic</span>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">data</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/ref</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#74a6f0227a087e1ff878da7036efea2a91d873c4"><strong>debian/ivar.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">docs/COOKBOOK.md</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">docs/MANUAL.md</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/README*</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">debian/tests/ref/README*</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#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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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#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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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#7bc9d38000a87c439477eb785ab5ff0f3ad425d0"><strong>debian/tests/ref/out-consensus.fa</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>Consensus_out-consensus_threshold_0_quality_20</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#853420e72aaad43223ece5fe7da669f0a3dc71e2"><strong>debian/tests/ref/out-consensus.qual.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#6aebea60053c51ab244c59087f6f4b5e330605c9"><strong>debian/tests/ref/out-filtered.tsv</strong></a>
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<li id="ad3ec2e85d99f99d65ad6e0f90dcdb2437ce00b4">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#ad3ec2e85d99f99d65ad6e0f90dcdb2437ce00b4"><strong>debian/tests/ref/out-getmasked.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">WNV_400_2_LEFT WNV_400_2_LEFT_alt WNV_400_1_LEFT WNV_400_1_LEFT_alt WNV_400_3_LEFT</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#7bc69b6e3ac4479f33997cb4cb0d12d9e6282173"><strong>debian/tests/ref/out-removereads.sam</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test_20_381_1:0:0_6:0:0_1_150 163 test 31 60 11S139M = 232 362 CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT <>VG?UM[8R5:A7PL<>5AL>RZ5BH[EDFOUP?VHRHJ<UVE:NQ@WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9@GQ8N7U;YF[MJFTQF[FZCM>TNDXGK\=AIZW=X=V?;7K:7A<JDUTJSTGFES5\D; RG:Z:Paired_Group_1_assembled_against_test XA:i:0</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">test_20_381_1:0:0_6:0:0_1_150 83 test 232 60 1M3D112M2D3M29S = 20 -357 TGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACTGAAACGATGCGGGGGAGGCCATATCTTCCAACCACATTGGGGTTGAATAAGTGGTTGAT ;SEFGTSJTUDJ<A7:K7;?V=X=WZIA=\KGXDNT>MCZF[FQTFJM[FY;U7N8QG@9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW@QN:EVU<JHRHV?OFDE[HB5ZR>LA5><LP7A:5R8[MU?GV>< RG:Z:Paired_Group_1_assembled_against_test XA:i:7</span></pre>
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<li id="0f2cd49c57122b0dfc6f125dfe43024beafd70c3">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#0f2cd49c57122b0dfc6f125dfe43024beafd70c3"><strong>debian/tests/ref/out-trim.sam</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test_20_381_1:0:0_6:0:0_1_150 163 test 31 60 11S139M = 232 362 CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT <>VG?UM[8R5:A7PL<>5AL>RZ5BH[EDFOUP?VHRHJ<UVE:NQ@WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9@GQ8N7U;YF[MJFTQF[FZCM>TNDXGK\=AIZW=X=V?;7K:7A<JDUTJSTGFES5\D; RG:Z:Paired_Group_1_assembled_against_test XA:i:0</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">test_20_381_1:0:0_6:0:0_1_150 83 test 232 60 1M3D112M2D3M29S = 20 -357 TGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACTGAAACGATGCGGGGGAGGCCATATCTTCCAACCACATTGGGGTTGAATAAGTGGTTGAT ;SEFGTSJTUDJ<A7:K7;?V=X=WZIA=\KGXDNT>MCZF[FQTFJM[FY;U7N8QG@9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW@QN:EVU<JHRHV?OFDE[HB5ZR>LA5><LP7A:5R8[MU?GV>< RG:Z:Paired_Group_1_assembled_against_test XA:i:7</span></pre>
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<li id="74eed610839f406a622a4f3dd20cd18eacef0d34">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#74eed610839f406a622a4f3dd20cd18eacef0d34"><strong>debian/tests/ref/out-trim2.sam</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test_20_381_1:0:0_6:0:0_1_150 163 test 31 60 11S139M = 232 362 CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT <>VG?UM[8R5:A7PL<>5AL>RZ5BH[EDFOUP?VHRHJ<UVE:NQ@WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9@GQ8N7U;YF[MJFTQF[FZCM>TNDXGK\=AIZW=X=V?;7K:7A<JDUTJSTGFES5\D; RG:Z:Paired_Group_1_assembled_against_test XA:i:0</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">test_20_381_1:0:0_6:0:0_1_150 83 test 232 60 1M3D112M2D3M29S = 20 -357 TGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACTGAAACGATGCGGGGGAGGCCATATCTTCCAACCACATTGGGGTTGAATAAGTGGTTGAT ;SEFGTSJTUDJ<A7:K7;?V=X=WZIA=\KGXDNT>MCZF[FQTFJM[FY;U7N8QG@9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW@QN:EVU<JHRHV?OFDE[HB5ZR>LA5><LP7A:5R8[MU?GV>< RG:Z:Paired_Group_1_assembled_against_test XA:i:7</span></pre>
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<li id="058d50901ea09a7dea6c514c76687de20eb9ce8a">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#058d50901ea09a7dea6c514c76687de20eb9ce8a"><strong>debian/tests/ref/out-variants.tsv</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/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241#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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4
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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>ivar</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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6
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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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9
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</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 class="nb" style="color: #0086b3;">ls</span> <span class="nt" style="color: #000080;">-R</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</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;">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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">ivar trim <span class="nt" style="color: #000080;">-i</span> data/test.sorted.bam <span class="nt" style="color: #000080;">-b</span> data/test.bed <span class="nt" style="color: #000080;">-p</span> out-trim</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">samtools view out-trim.bam <span class="o" style="font-weight: 600;">></span> out-trim.sam</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">diff out-trim.sam ref/out-trim.sam</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;">[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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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>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">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="LC30" class="line" lang="shell">ivar trim <span class="nt" style="color: #000080;">-i</span> data/test.sorted.bam <span class="nt" style="color: #000080;">-b</span> data/test.bed <span class="nt" style="color: #000080;">-p</span> out-trim2 <span class="nt" style="color: #000080;">-q</span> 15 <span class="nt" style="color: #000080;">-m</span> 50 <span class="nt" style="color: #000080;">-s</span> 4</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">samtools view out-trim2.bam <span class="o" style="font-weight: 600;">></span> out-trim2.sam</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">diff out-trim2.sam ref/out-trim2.sam</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="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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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>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" 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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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">samtools mpileup <span class="nt" style="color: #000080;">-A</span> <span class="nt" style="color: #000080;">-d</span> 600000 <span class="nt" style="color: #000080;">-B</span> <span class="nt" style="color: #000080;">-Q</span> 0 data/test.trimmed.sorted.bam | ivar variants <span class="nt" style="color: #000080;">-p</span> out-variants <span class="nt" style="color: #000080;">-q</span> 20 <span class="nt" style="color: #000080;">-t</span> 0.03</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">diff out-variants.tsv ref/out-variants.tsv</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 4</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">ivar filtervariants <span class="nt" style="color: #000080;">-t</span> 0.5 <span class="nt" style="color: #000080;">-p</span> out-filtered out-variants.tsv</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell">diff out-variants.tsv ref/out-variants.tsv</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>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"></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 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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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell">samtools mpileup <span class="nt" style="color: #000080;">-d</span> 1000 <span class="nt" style="color: #000080;">-A</span> <span class="nt" style="color: #000080;">-Q</span> 0 data/test.sorted.bam | ivar consensus <span class="nt" style="color: #000080;">-p</span> out-consensus <span class="nt" style="color: #000080;">-q</span> 20 <span class="nt" style="color: #000080;">-t</span> 0</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell">diff out-consensus.qual.txt ref/out-consensus.qual.txt</span>
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51
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<pre style="margin: 0;">+<span id="LC51" 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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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" 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 6</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="LC55" class="line" lang="shell">ivar getmasked <span class="nt" style="color: #000080;">-i</span> data/test.filtered.tsv <span class="nt" style="color: #000080;">-b</span> data/test.bed <span class="nt" style="color: #000080;">-f</span> data/out-filtered.tsv <span class="nt" style="color: #000080;">-p</span> out-getmasked</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell">diff out-getmasked.txt ref/out-getmasked.txt</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="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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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>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" 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 7</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="LC61" class="line" lang="shell">ivar removereads <span class="nt" style="color: #000080;">-i</span> out-trim.bam <span class="nt" style="color: #000080;">-p</span> out-removereads <span class="nt" style="color: #000080;">-t</span> data.out-getmasked.txt <span class="nt" style="color: #000080;">-b</span> data/test.bed</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell">samtools view out-removereads.bam <span class="o" style="font-weight: 600;">></span> out-removereads.sam</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell">diff out-removereads.sam ref/out-removereads.sam</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 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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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"></span></pre>
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