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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/fitgcp">Debian Med / fitgcp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/-/commit/bef305592f794be4ad9252384a2633e59a3a3862">bef30559</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-11T21:24:27+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/-/commit/db3098de876a2204b8b03bdae60c79b482fb9803">db3098de</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-11T21:25:26+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/-/commit/25451d295588d809989fc87cbc3c59069f8e35e0">25451d29</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-11T21:57:11+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some changes that 2to3 probably missed
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/-/commit/6c6449c5454b7ff76b76beefbb6134664bf8a929">6c6449c5</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-11T23:23:45+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install sources and docs
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/-/commit/3b470dc33cf5c3aae564ef26f1621dd1a01bfc81">3b470dc3</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-12T02:31:23+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add more autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fitgcp/-/commit/a1b3c6db184655b706e1df70e2013d0b6b48b064">a1b3c6db</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-05-12T02:32:57+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
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</li>
<li class="file-stats">
<a href="#55c6cad22b6520d6afd07b52ff22bcd42320cfb0">
<span class="new-file">
+
debian/patches/2to3_additions.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#a2a565aa25c2bf10949e3702636a59d9f1110a11">
<span class="new-file">
+
debian/tests/README.test_data
</span>
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
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</li>
<li class="file-stats">
<a href="#168f95cb3f25a345ecc0cca89270c923034b9bad">
<span class="new-file">
+
debian/tests/data/NC_004830.2.sam
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</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fitgcp (0.0.20150429-4) 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"> [ Steffen Möller ]</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Could not find ref to conda</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"> [ Steffen Moeller ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * d/u/metadata: yamllint</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Pranav Ballaney ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Add examples</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Some changes that 2to3 probably missed</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Install sources and docs</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Add more autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Tue, 12 May 2020 02:32:07 +0530</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">fitgcp (0.0.20150429-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README*</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/README.test_data</span></pre>
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<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#55c6cad22b6520d6afd07b52ff22bcd42320cfb0"><strong>debian/patches/2to3_additions.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Some changes that 2to3 probably missed</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pranav Ballaney <ballaneypranav@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Tue, 11 May 2020 21:53:00 +0530</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/fitGCP.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/fitGCP.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -128,7 +128,7 @@</span> class NBinom(Distribution):</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> return stats.nbinom.pmf(x,self._p1,self._p2)</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> def estimate_par(self, data, weights=None):</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if weights == None:</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if weights is None:</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> weights = data*0. + 1.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> norm = np.sum(weights)</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> mean = np.sum(data*weights)/(norm + 10**(-25))</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -338,7 +338,7 @@</span> class DataSet:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> def read_from_pickle(self,filename):</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> """ read a genome coverage profile from a pickle file. """</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- data = pickle.load(open(filename,'r'))</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ data = pickle.load(open(filename,'rb'))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> self.cov = np.array(data[0],dtype=np.int)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> self.count = np.array(data[1],dtype=np.int)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -363,7 +363,7 @@</span> class DataSet:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> if not read.is_unmapped:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> r_start = start_pos[read.tid] + read.pos # start position </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> r_end = start_pos[read.tid] + read.pos + read.qlen # end </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cov[r_start:r_end] += 1 </span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cov[int(r_start):int(r_end)] += 1</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> num_reads += 1</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> read_length += r_end-r_start</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> self.fname = filename</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -376,7 +376,7 @@</span> class DataSet:</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> def write_to_pickle(self, filename):</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> """ store dataset in a pickle file. """</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> return pickle.dump([self.cov, self.count, self.rlen, self.rds,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.glen, self.fname], open(filename,'w'))</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.glen, self.fname], open(filename,'wb'))</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -446,11 +446,11 @@</span> def iterative_fitting(data_set, mixture_</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> # maximum CDF difference</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> xs = np.arange(np.max(data_set.cov)+1)</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ref_pdf = np.zeros((np.max(data_set.cov)+1,))</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ref_pdf = np.zeros((int(np.max(data_set.cov))+1,))</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> for dist in mixture_model:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> ref_pdf += dist.pmf(xs)*dist.alpha</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- obs_pdf = np.zeros((np.max(data_set.cov)+1,))</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ obs_pdf = np.zeros((int(np.max(data_set.cov))+1,))</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> obs_pdf[data_set.cov.astype(np.int)] = data_set.count/float(np.sum(data_set.count))</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> max_cdf_diff = np.max(np.abs(np.cumsum(ref_pdf)-np.cumsum(obs_pdf)))</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2to3_additions.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#a2a565aa25c2bf10949e3702636a59d9f1110a11"><strong>debian/tests/README.test_data</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">File: NC_004830.2.sam</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">This file was obtained using mason and bowtie as described </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">in the supplementary data for the following publication:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> http://dx.doi.org/10.1093/bioinformatics/btt147</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">A fasta file was downloaded from:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> https://www.ncbi.nlm.nih.gov/nuccore/NC_004830</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">and the following operations were performed on it: </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> mason illumina -N 100000 -n 75 -sq -o NC_004830.2.fastq NC_004830.2.fa</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> bowtie -p 20 -q -k 1 -S NC_004830.2.fa NC_004830.2.fastq NC_004830.2.sam</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">-- Pranav Ballaney <ballaneypranav@gmail.com></span></pre>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, python3-matplotlib</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#168f95cb3f25a345ecc0cca89270c923034b9bad"><strong>debian/tests/data/NC_004830.2.sam</strong></a>
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<a href="https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>fitgcp</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">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: Verbose with a plot</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">fitgcp <span class="nt" style="color: #000080;">-l</span> <span class="nt" style="color: #000080;">-p</span> NC_004830.2.sam</span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"NC_004830.2_zn.png"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"NC_004830.2_zn_log.txt"</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;">test</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"NC_004830.2_zn_results.txt"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm </span>NC_004830.2_zn.png NC_004830.2_zn_log.txt NC_004830.2_zn_results.txt</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="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="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC30" 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: Only ten iterations</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">fitgcp <span class="nt" style="color: #000080;">-i</span> 10 NC_004830.2.sam</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-f</span> NC_004830.2_zn_results.txt</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[92m</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[1mPassed</span><span class="se" style="color: #d14;">\e</span><span class="s2" style="color: #d14;">[0m"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span></pre>
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