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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/minia">Debian Med / minia</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/add5770faf8c4129213e46de627d197871d8712d">add5770f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-16T08:23:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port from Python2 to Python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/4cc33eb53c739233570c10fe214a21d86232f5a7">4cc33eb5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-16T08:26:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Latest update also fixed autopkgtest issue
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/minia/commit/fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d">fa6e0cee</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-16T08:30:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#779b26fdbe829ccbab626b9bf143e14363666e5f">
debian/patches/link_libraries.patch
</a>
</li>
<li class="file-stats">
<a href="#aba6ac4aa9f431d593f6ca438e03f75f7e78c8fd">
debian/patches/no_install_to_wrong_dir.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#ef912d182f7242560f1051f726bb4e67c96eeab5">
debian/patches/skip-rpath.patch
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</li>
<li class="file-stats">
<a href="#617a6ef0dc813d1ce3f6df69d5f39b1fc3f73294">
debian/patches/use_debian_packaged_gatb-core.patch
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">minia (3.2.1+git20191130.5b131b9-2) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use 2to3 to port from Python2 to Python3</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"> Closes: #943115</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="plaintext"> * Latest update also fixed autopkgtest issue</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Closes: #939894</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 16 Dec 2019 09:26:55 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="10" 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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">minia (3.2.1+git20191130.5b131b9-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="12" 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">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port from Python2 to Python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/943115 </span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Mon, 16 Dec 2019 09:21:08 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/scripts/convertToGFA.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/convertToGFA.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> '''****************************************************************************</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -20,8 +20,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> '''****************************************************************************</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"><span class="gd" style="color: #000; background-color: #fdd;">-* To run the program, pass three arguments with the python script on command line.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-* For example - python convertToGFA.py inputFileName outputFileName kmerSize</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+* To run the program, pass three arguments with the python3 script on command line.</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;">+* For example - python3 convertToGFA.py inputFileName outputFileName kmerSize</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"> * Logic - It reads through the fasta file with all the unitigs information </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> * and link information and outputs it in the GFA format. </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/debug_1seq_tip_removal.py</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/debug_1seq_tip_removal.py</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -16,7 +16,7 @@</span> for line in fasta:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> seq = line.strip()</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> is_error = False</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> is_genome = False</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(len(seq)-k+1):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(seq)-k+1):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> kmer = seq[i:i+k]</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> if kmer not in genome[0] and kmer not in genome[1]:</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> is_error = True</span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -24,9 +24,9 @@</span> for line in fasta:</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> is_genome = True</span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if is_error and is_genome:</span>
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<td class="diff-line-num new new_line" data-linenumber="40" 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">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "mix of erroneous kmers and true genomic kmers inside the same assembled contig!!"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print id</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print seq</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("mix of erroneous kmers and true genomic kmers inside the same assembled contig!!")</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(id)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(seq)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> exit(1)</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> else:</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print id,is_error,is_genome</span></span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(id,is_error,is_genome)</span></span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/duplicate_sequences_according_abundance.py</span></span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/duplicate_sequences_according_abundance.py</span></span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span> for line in fasta:</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> #print abundance</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> id=line</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="55" 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">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(int(abundance)):</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print id,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print line,</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(int(abundance)):</span></span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(id, end=' ')</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(line, end=' ')</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/ilots_stats.py</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/ilots_stats.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -37,4 +37,4 @@</span> for ctg in ctg_connect:</span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> nb_ilots += 1</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print "contigs input", nb_ctg/2, "connected", nb_connected, "ilots", nb_ilots</span></span>
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<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print("contigs input", nb_ctg/2, "connected", nb_connected, "ilots", nb_ilots)</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/max_mem_usage_from_log.py</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/max_mem_usage_from_log.py</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -10,4 +10,4 @@</span> for line in sys.stdin:</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> mem=int(s[i-1])</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> max_mem=max(mem,max_mem)</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print max_mem</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(max_mem)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/strip_bcalm_links.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/strip_bcalm_links.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -3,11 +3,11 @@</span> file=sys.argv[1]</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> for line in open(file):</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> line=line.strip()</span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> if not line.startswith(">"):</span>
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<td class="diff-line-num new new_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(line.strip())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((line.strip()))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" 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">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> continue</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> if "L:" in line:</span>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="diff-line-num new new_line" data-linenumber="89" 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">
89
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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="LC89" class="line" lang="diff"> s = line.split("L:")</span>
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<td class="diff-line-num new new_line" data-linenumber="90" 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">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" 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">
91
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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="LC91" class="line" lang="diff"> s = [line.strip()]</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="diff-line-num new new_line" data-linenumber="92" 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">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print(s[0])</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" 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">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print((s[0]))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" 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">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/compare_fasta.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/compare_fasta.py</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -32,5 +32,5 @@</span> if len(s1) == len(s2) and len(s1) == 1:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> else:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> print("BAD: one sequence doesn't exactly match the other")</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print("NOT EQUAL: %d sequence(s) in %s not in %s" % (len(s1.difference(s2)), fasta1, fasta2))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+print(("NOT EQUAL: %d sequence(s) in %s not in %s" % (len(s1.difference(s2)), fasta1, fasta2)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> sys.exit(1)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/simple_test.sh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/simple_test.sh</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span> function test()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> else</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> eval $bindir/minia $args</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> fi</span>
</pre>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python compare_fasta.py "$file".solution.fa "$file".contigs.fa</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 compare_fasta.py "$file".solution.fa "$file".contigs.fa</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> # Test One</span></pre>
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<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#779b26fdbe829ccbab626b9bf143e14363666e5f"><strong>debian/patches/link_libraries.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Description: Link against Debian packaged gatbcore</td>
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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/CMakeLists.txt</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/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left right">2,15 +72,17 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left">4,15 +74,17 @@</span></span><span class="idiff right"> cmake_policy(SET CMP0009 NEW) # fixes cm</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> include_directories (${PROGRAM_SOURCE_DIR})</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> file (GLOB_RECURSE ProjectFiles ${PROGRAM_SOURCE_DIR}/*)</span>
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<li id="aba6ac4aa9f431d593f6ca438e03f75f7e78c8fd">
<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#aba6ac4aa9f431d593f6ca438e03f75f7e78c8fd"><strong>debian/patches/no_install_to_wrong_dir.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Description: Failed to fix these install dirs, deactivate completely and use dh_</td>
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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/CMakeLists.txt</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/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left right">7,9 +127,9 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left">9,9 +129,9 @@</span></span><span class="idiff right"> SET (CPACK_SOURCE_IGNORE_FILES</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> # We copy the project binary to the 'bin' directory</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,3 +3,4 @@ link_libraries.patch</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">no_install_to_wrong_dir.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">skip-rpath.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">fix_path_in_tests.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">2to3.patch</span></pre>
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<li id="ef912d182f7242560f1051f726bb4e67c96eeab5">
<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#ef912d182f7242560f1051f726bb4e67c96eeab5"><strong>debian/patches/skip-rpath.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Description: Do not set rpath</td>
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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/CMakeLists.txt</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/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left right">5,6 +75</span>,7 @@</span> file (GLOB_RECURSE ProjectFiles ${PROG</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left right">7,6 +77</span>,7 @@</span> file (GLOB_RECURSE ProjectFiles ${PROG</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> include(GNUInstallDirs)</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> add_executable(${PROJECT_NAME} ${ProjectFiles})</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Description: Do not set rpath</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> target_link_libraries(${PROJECT_NAME} gatbcore hdf5 )</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> # merci</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left right">2,6 +83</span>,7 @@</span> set (MERCI_SOURCE_DIR ${PROJECT_SOURCE_D</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left right">4,6 +85</span>,7 @@</span> set (MERCI_SOURCE_DIR ${PROJECT_SOURCE_D</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> include_directories (${MERCI_SOURCE_DIR})</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> file (GLOB_RECURSE MerciFiles ${MERCI_SOURCE_DIR}/*.cpp)</span>
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<td class="diff-line-num old_line" data-linenumber="18" 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">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> add_executable("merci" ${MerciFiles})</span>
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<li id="617a6ef0dc813d1ce3f6df69d5f39b1fc3f73294">
<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#617a6ef0dc813d1ce3f6df69d5f39b1fc3f73294"><strong>debian/patches/use_debian_packaged_gatb-core.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Last-Update: Mon, 21 Jan 2019 09:01:19 +0100</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Use cmake input file of Debian packaged gatb-core</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -28,20 +28,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -28,20 +28,6 @@</span><span class="idiff left right"> IF (DEFINED JENKINS_TAG)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> SET (gatb-tool-version ${JENKINS_TAG})</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> ENDIF()</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" 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>
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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">@@ -24,7 +24,7 @@ Description: Use cmake input file of Debian packaged gatb-core</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> # Define cmake modules directory</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> ################################################################################</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -66,7 +52,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -66,7 +52,7 @@</span><span class="idiff left right"> SET (GATB_CORE_EXCLUDE_TESTS 1)</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> SET (GATB_CORE_EXCLUDE_EXAMPLES 1)</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> # GATB CORE</span>
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<a href="https://salsa.debian.org/med-team/minia/compare/b6cc8e8152b5fda7949ea2f3878aa62d47dd7730...fa6e0ceebb96e86e2e01f53f4e219ed8dfb91a1d#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, samtools, python, bandage</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, samtools, python<span class="idiff left right">3</span>, bandage</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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