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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/jellyfish">Debian Med / jellyfish</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/8cac4aa0bb2afde98f5e1672cc0005565ba91e14">8cac4aa0</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2018-03-12T05:22:40-07:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add the missing small_mers.sh file, courtesy upstream.
</pre>
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<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/3952220cbaca160a19165bc19ea655ab5f66a6bc">3952220c</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2018-03-12T05:31:14-07:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add fix from upstream for arm/ppc
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#623e1fe488a7ff64fb7b06d083c94bb47d0555a6">
<span class="new-file">
+
debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
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<li class="file-stats">
<a href="#dcf0532af16131e0f0d1f1b3d83276265b242593">
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+
debian/patches/add_small_mers.sh.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#6b978c8ad7242d2a071fec666526fb8b68a0aab1">
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−
debian/patches/skip_small_mers.sh
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">jellyfish (2.2.8-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Add the missing small_mers.sh file, courtesy upstream.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Fix arm/powerpc build, patch courtesy upstream (Closes: #890137)</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"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 12 Mar 2018 05:31:00 -0700</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">jellyfish (2.2.8-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * New upstream version</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: JELLYFISH</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Upstream-Contact: Guillaume Marçais <gmarcais@umd.edu></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: http://www.cbcb.umd.edu/software/jellyfish/</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,6 @@ Files: *</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Copyright: Copyright 2011-2014 Guillaume Marçais1, Carl Kingsford</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: GPL-3+</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Files: jellyfish/randomc.h</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: Copyright 2008 Agner Fog</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">License: GPL</span>
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<li id="623e1fe488a7ff64fb7b06d083c94bb47d0555a6">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc#623e1fe488a7ff64fb7b06d083c94bb47d0555a6"><strong>debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">>From 6dfc57b516249454dc0a708ceb4833623cbf0ffd Mon Sep 17 00:00:00 2001</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">From: Guillaume Marcais <gmarcais@cs.cmu.edu></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Date: Wed, 14 Feb 2018 07:29:54 -0500</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Subject: [PATCH] Fix testing on arm64.</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">---</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> jellyfish/fastq2sam.cc | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</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"><span class="gh" style="color: #999;">diff --git a/jellyfish/fastq2sam.cc b/jellyfish/fastq2sam.cc</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">index e152ccf..b0b6b0d 100644</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/jellyfish/fastq2sam.cc</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/jellyfish/fastq2sam.cc</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -25,7 +25,7 @@ int main(int argc, char* argv[]) {</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> // os << "@PG\tID:fastq2sam\tPN:fastq2sam\n";</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"> std::string name, seq, quals;</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;">- char c = is.get();</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int c = is.get();</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> while(c == '@') {</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> std::getline(is, name);</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> std::getline(is, seq);</span></pre>
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<li id="dcf0532af16131e0f0d1f1b3d83276265b242593">
<a href="https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc#dcf0532af16131e0f0d1f1b3d83276265b242593"><strong>debian/patches/add_small_mers.sh.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">>From 0adb7ea223a6718bad4e82fc9813ae7708b59ee2 Mon Sep 17 00:00:00 2001</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">From: Guillaume Marcais <gmarcais@cs.cmu.edu></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Date: Mon, 12 Feb 2018 14:32:29 -0500</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Subject: [PATCH] Added missing tests/small_mers.sh file.</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">---</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> tests/small_mers.sh | 11 +++++++++++</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 1 file changed, 11 insertions(+)</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> create mode 100644 tests/small_mers.sh</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/tests/small_mers.sh b/tests/small_mers.sh</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">new file mode 100644</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gh" style="color: #999;">index 0000000..5eb7db0</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/small_mers.sh</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -0,0 +1,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#! /bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+cd tests</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;">+. ./compat.sh</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+sort -k2,2 > ${pref}.md5sum <<EOF</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EOF</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$JF count -t $nCPUs -o ${pref}_m10_10M.jf -s 1M -m 7 -C seq10m.fa</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+$JF histo ${pref}_m10_10M.jf > ${pref}_m10_10M.histo</span></span></pre>
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<a href="https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc#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">@@ -6,4 +6,5 @@ spelling</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">gcc-7.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">reproducible.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">portability.patch</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">skip_small_mers.sh</span></pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">add_small_mers.sh.patch</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/jellyfish/compare/c2cdb414c927d03d225db69bacd80490554c75fb...3952220cbaca160a19165bc19ea655ab5f66a6bc#6b978c8ad7242d2a071fec666526fb8b68a0aab1"><strong>debian/patches/skip_small_mers.sh</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell">Description: Skip missing <span class="nb" style="color: #0086b3;">test </span>file from upstream</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nt" style="color: navy;">---</span> jellyfish.orig/Makefile.am</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell">+++ jellyfish/Makefile.am</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell">@@ <span class="nt" style="color: navy;">-146</span>,8 +146,7 @@</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"> TESTS <span class="o" style="font-weight: 600;">=</span> tests/generate_sequence.sh tests/parallel_hashing.sh <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"> tests/merge.sh tests/bloom_filter.sh tests/big.sh <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> tests/subset_hashing.sh tests/multi_file.sh <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell">- tests/bloom_counter.sh tests/large_key.sh tests/sam.sh <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell">- tests/small_mers.sh</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell">+ tests/bloom_counter.sh tests/large_key.sh tests/sam.sh</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"> </span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"> EXTRA_DIST +<span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">$(</span>TESTS<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"> clean-local: clean-local-check</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell">@@ <span class="nt" style="color: navy;">-165</span>,7 +164,6 @@</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"> tests/large_key.log: tests/generate_sequence.log</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"> tests/quality_filter.log: tests/generate_sequence.log</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"> tests/sam.log: tests/generate_sequence.log</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nt" style="color: navy;">-tests</span>/small_mers.log: tests/generate_sequence.log</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># SWIG tests</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> TESTS +<span class="o" style="font-weight: 600;">=</span> tests/swig_python.sh tests/swig_ruby.sh tests/swig_perl.sh</span></pre>
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