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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/htsjdk">Debian Med / htsjdk</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a">b43e04ad</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2022-02-18T22:22:33+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding autopkgtests for the majority of reverse-dependencies
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<h4>10 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<a href="#68ebf8e432d3148e17e4c5f6ff293006b1d4932a">
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debian/tests/beagle-run-sample-analysis
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<a href="#7c34b05f725a595f2f005817bffde3ccf53a2234">
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debian/tests/chromhmm-run-sample-analysis
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<li class="file-stats">
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debian/tests/control
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<a href="#4e8bcc310adc4f4ef3581fa29fed8571342c0cba">
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debian/tests/drop-seq-run-unit-test
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debian/tests/fastqc-run-unit-test
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debian/tests/jalview-run-unit-test
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debian/tests/picard-tools-run-unit-test
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<a href="#a1166ffdd65bec9ddaa78c5c42d04b7933f3587f">
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debian/tests/pilon-run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">htsjdk (2.24.1+dfsg-2) 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"> * Adding autopkgtests to test reverse-dependencies when upgrading htsjdk</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #920588</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> TODO: add tests for other reverse-dependencies.</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"> -- Pierre Gruet <pgt@debian.org> Fri, 18 Feb 2022 15:50:28 +0100</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">htsjdk (2.24.1+dfsg-1) 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"> [ Olivier Sallou ]</span>
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<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,9 +157,35 @@ Copyright: 2010 Shaun Jackman <sjackman@debian.org></td>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="plaintext"> 2013-2018 Olivier Sallou <osallou@debian.org></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"> 2015 Vincent Danjean <vdanjean@debian.org></span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext">License: ISC</span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"> Permission to use, copy, modify, and/or distribute this software for any</span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"> purpose with or without fee is hereby granted, provided that the above</span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext"> copyright notice and this permission notice appear in all copies.</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">Files: debian/tests/beagle-run-sample-analysis</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> debian/tests/chromhmm-run-sample-analysis</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">Copyright: 2016-2021 Dylan Aïssi <daissi@debian.org></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">License: Expat</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">Comment: These files come from the packages beagle and chromhmm, licenses were</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> changed from GPL-3+ to Expat after discussion with the copyright holder.</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">Files: debian/tests/drop-seq-run-unit-test</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> debian/tests/pilon-run-unit-test</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">Copyright: 2020 Andreas Tille <tille@debian.org></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">License: Expat</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">Files: debian/tests/fastqc-run-unit-test</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">Copyright: 2012 Steffen Moeller <moeller@debian.org></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">License: Expat</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">Comment: This file comes from the package fastqc, the license was changed from</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> GPL-3+ to Expat after discussion with the copyright holder.</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">Files: debian/tests/jalview-run-unit-test</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">Copyright: 2020-2021 Pierre Gruet <pgt@debian.org></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">License: Expat</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">Files: debian/tests/picard-tools-run-unit-test</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">Copyright: 2010 Shaun Jackman <sjackman@debian.org></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> 2013-2018 Olivier Sallou <osallou@debian.org></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> 2015-2016 Vincent Danjean <vdanjean@debian.org></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> 2016-2018 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="plaintext">License: Apache-2.0</span>
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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">@@ -289,3 +315,8 @@ License: Public-Domain</td>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="plaintext"> purpose.</span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="plaintext"> Please cite the author in any work or product based on this material.</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">License: ISC</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> copyright notice and this permission notice appear in all copies.</span></pre>
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<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#68ebf8e432d3148e17e4c5f6ff293006b1d4932a"><strong>debian/tests/beagle-run-sample-analysis</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># http://dep.debian.net/deps/dep8/</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Autopkgtest: Test if beagle run analysis correctly</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Author: Dylan Aïssi <daissi@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>beagle</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="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Generate necessary files</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gzip </span>test.vcf</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">zcat test.vcf.gz | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1-190</span> | <span class="nb" style="color: #0086b3;">tr</span> <span class="s1" style="color: #d14;">'/'</span> <span class="s1" style="color: #d14;">'|'</span> | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> ref.vcf.gz</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">zcat test.vcf.gz | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1-9</span>,191-200 | <span class="nb" style="color: #0086b3;">gzip</span> <span class="o" style="font-weight: 600;">></span> target.vcf.gz</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">bref3 ref.vcf.gz <span class="o" style="font-weight: 600;">></span> ref.bref3</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Beagle with gt argument</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">beagle <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>test.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.gt</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Beagle with ref and gt argument</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">beagle <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">=</span>ref.vcf.gz <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>target.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.ref</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Beagle with bref3 file</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">beagle <span class="nv" style="color: #008080;">ref</span><span class="o" style="font-weight: 600;">=</span>ref.bref3 <span class="nv" style="color: #008080;">gt</span><span class="o" style="font-weight: 600;">=</span>target.vcf.gz <span class="nv" style="color: #008080;">out</span><span class="o" style="font-weight: 600;">=</span>out.bref3</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span>/<span class="k" style="font-weight: 600;">*</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#7c34b05f725a595f2f005817bffde3ccf53a2234"><strong>debian/tests/chromhmm-run-sample-analysis</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>chromhmm</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Just print the version</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">ChromHMM Version</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Example from ChromHMM website</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">ChromHMM <span class="nt" style="color: #000080;">-mx1600M</span> LearnModel SAMPLEDATA_HG18 OUTPUTSAMPLE 10 hg18</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: beagle-run-sample-analysis</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: beagle, beagle-doc</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Architecture: !armhf</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Tests: chromhmm-run-sample-analysis</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Depends: chromhmm, chromhmm-example</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">Tests: drop-seq-run-unit-test</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Depends: drop-seq-tools, drop-seq-testdata, samtools</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Restrictions: allow-stderr, skip-not-installable</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Tests: fastqc-run-unit-test</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Depends: fastqc, unzip</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Tests: jalview-run-unit-test</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Depends: jalview</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Tests: picard-tools-run-unit-test</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Depends: picard-tools</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Restrictions: allow-stderr, skip-not-installable</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Tests: pilon-run-unit-test</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Depends: pilon</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<li id="4e8bcc310adc4f4ef3581fa29fed8571342c0cba">
<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#4e8bcc310adc4f4ef3581fa29fed8571342c0cba"><strong>debian/tests/drop-seq-run-unit-test</strong></a>
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1
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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>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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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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<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="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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<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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<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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<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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<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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<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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<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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<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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<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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<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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<td class="new_line diff-line-num new" data-linenumber="51" 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="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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<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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<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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<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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<li id="59dda0fc2d090e7de90aecd76e21ae98f1c01751">
<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#59dda0fc2d090e7de90aecd76e21ae98f1c01751"><strong>debian/tests/fastqc-run-unit-test</strong></a>
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1
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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><span class="s2" style="color: #d14;">"fastqc"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">test_failures</span><span class="o" style="font-weight: 600;">=</span>0</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></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="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</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="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC9" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gz"</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>sample <span class="k" style="font-weight: 600;">in </span>example.fastq toy_sam.sam toy_bam.bam <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> /usr/bin/fastqc <span class="nt" style="color: #000080;">--extract</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> <span class="nv" style="color: #008080;">result</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">sample</span><span class="p">%%.*</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_fastqc"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="nv" style="color: #008080;">expected</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">result</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_expected_summary.txt"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> diff <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">result</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">/summary.txt"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">expected</span><span class="k" style="font-weight: 600;">}</span> 2>/dev/null <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="o" style="font-weight: 600;">((</span> test_failures +<span class="o" style="font-weight: 600;">=</span> 1 <span class="o" style="font-weight: 600;">))</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Summary results did not match contents of </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">expected</span><span class="k" style="font-weight: 600;">}</span><span class="sh" style="color: #d14;"> for</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;"> fastqc "</span><span class="nv" style="color: #008080;">$sample</span><span class="sh" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;">Please investigate!</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Summary results match for: fastqc "</span><span class="nv" style="color: #008080;">$sample</span><span class="s2" style="color: #d14;">" "</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$result</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">*</span></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="s2" style="color: #d14;">""</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">((</span> test_failures <span class="o" style="font-weight: 600;">==</span> 0 <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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"FAIL mismatched fastqc summary count: </span><span class="nv" style="color: #008080;">$test_failures</span><span class="s2" style="color: #d14;">"</span></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;">exit </span>1</span></pre>
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<li id="8191d6a9db7953068052403c8af031775cc1125d">
<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#8191d6a9db7953068052403c8af031775cc1125d"><strong>debian/tests/jalview-run-unit-test</strong></a>
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1
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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>jalview</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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">jalview <span class="nt" style="color: #000080;">-nodisplay</span> <span class="nt" style="color: #000080;">-open</span> uniref50.fa <span class="nt" style="color: #000080;">-eps</span> uniref50_out.eps</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Output generated in eps format in </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">/uniref50_out.eps"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Failed to generate output in eps format"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">jalview <span class="nt" style="color: #000080;">-nodisplay</span> <span class="nt" style="color: #000080;">-open</span> uniref50.fa <span class="nt" style="color: #000080;">-html</span> uniref50_out.html</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <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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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Output generated in html format in </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">/uniref50_out.html"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Failed to generate output in eps format"</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;">exit </span>1</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">jalview <span class="nt" style="color: #000080;">-nodisplay</span> <span class="nt" style="color: #000080;">-open</span> uniref50.fa <span class="nt" style="color: #000080;">-png</span> uniref50_out.png</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <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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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Output generated in png format in </span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">/uniref50_out.png"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Failed to generate output in png format"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<li id="22370772890870d2d1a3f9a178f92124cb8309b4">
<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#22370772890870d2d1a3f9a178f92124cb8309b4"><strong>debian/tests/picard-tools-run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>picard-tools</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></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;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/unmapped.sam <span class="nb" style="color: #0086b3;">.</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/mini.vcf<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="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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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">PicardCommandLine ViewSam <span class="nv" style="color: #008080;">PF_STATUS</span><span class="o" style="font-weight: 600;">=</span>All <span class="nv" style="color: #008080;">ALIGNMENT_STATUS</span><span class="o" style="font-weight: 600;">=</span>All <span class="nv" style="color: #008080;">INPUT</span><span class="o" style="font-weight: 600;">=</span>unmapped.sam</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">PicardCommandLine CollectSequencingArtifactMetrics <span class="nv" style="color: #008080;">I</span><span class="o" style="font-weight: 600;">=</span>test.sam <span class="nv" style="color: #008080;">O</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">test </span><span class="nv" style="color: #008080;">R</span><span class="o" style="font-weight: 600;">=</span>test.fasta</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nv" style="color: #008080;">o1</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"test.bait_bias_detail_metrics"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">o2</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"test.bait_bias_summary_metrics"</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">o3</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"test.error_summary_metrics"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nv" style="color: #008080;">o4</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"test.pre_adapter_detail_metrics"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nv" style="color: #008080;">o5</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"test.pre_adapter_summary_metrics"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$o1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$o2</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$o3</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$o4</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$o5</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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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"All output files generated"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Some files are not generated"</span> <span class="o" style="font-weight: 600;">></span>&2</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;">exit </span>1</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">PicardCommandLine SortVcf <span class="nv" style="color: #008080;">I</span><span class="o" style="font-weight: 600;">=</span>mini.vcf <span class="nv" style="color: #008080;">O</span><span class="o" style="font-weight: 600;">=</span>mini_sorted.vcf</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="nv" style="color: #008080;">out_vcf</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"mini_sorted.vcf"</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$out_vcf</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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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"sorted vcf generated"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"sorted vcf haven't been generated"</span> <span class="o" style="font-weight: 600;">></span>&2</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;">exit </span>1</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell">PicardCommandLine SplitVcfs <span class="nv" style="color: #008080;">I</span><span class="o" style="font-weight: 600;">=</span>mini.vcf <span class="nv" style="color: #008080;">SNP_OUTPUT</span><span class="o" style="font-weight: 600;">=</span>snp.vcf <span class="nv" style="color: #008080;">INDEL_OUTPUT</span><span class="o" style="font-weight: 600;">=</span>indel.vcf</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nv" style="color: #008080;">out_snp</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"snp.vcf"</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nv" style="color: #008080;">out_indel</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"indel.vcf"</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="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$out_snp</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$out_indel</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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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"snp and indel vcfs generated"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"not all output files have been generated"</span> <span class="o" style="font-weight: 600;">></span>&2</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;">exit </span>1</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span></pre>
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<li id="a1166ffdd65bec9ddaa78c5c42d04b7933f3587f">
<a href="https://salsa.debian.org/med-team/htsjdk/-/commit/b43e04ad5247e67ea960753ee618847086210d6a#a1166ffdd65bec9ddaa78c5c42d04b7933f3587f"><strong>debian/tests/pilon-run-unit-test</strong></a>
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1
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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>pilon</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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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">pilon <span class="nt" style="color: #000080;">--genome</span> NC_045512.2.fasta <span class="nt" style="color: #000080;">--bam</span> SRR11728627.sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">diff pilon.fasta ref/pilon.fasta </span></pre>
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