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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/jellyfish">Debian Med / jellyfish</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a">ea26fa3a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-03T06:56:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up quilt patches
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#623e1fe488a7ff64fb7b06d083c94bb47d0555a6">
<span class="deleted-file">
−
debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#dcf0532af16131e0f0d1f1b3d83276265b242593">
<span class="deleted-file">
−
debian/patches/add_small_mers.sh.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#76ce9724ed97a005df2dfe559d65dc1c62f53c3f">
<span class="deleted-file">
−
debian/patches/drop-rpath
</span>
</a>
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<li class="file-stats">
<a href="#1cc4b89414889f6673c04af83da7a47f7be14f5a">
<span class="deleted-file">
−
debian/patches/gcc-7.patch
</span>
</a>
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<li class="file-stats">
<a href="#87d775dfc70cd7349d92999c3cf4ecef0ce8e99f">
<span class="deleted-file">
−
debian/patches/modern-g++
</span>
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<li class="file-stats">
<a href="#e29b151bd5860ac92a6c8994a6ea279159e34d37">
<span class="deleted-file">
−
debian/patches/pkg-config-with-name
</span>
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="deleted-file">
−
debian/patches/spelling
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,10 +4,11 @@ jellyfish (2.2.10-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="4" 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">
4
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<td class="diff-line-num new_line" data-linenumber="4" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
</pre>
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5
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<td class="diff-line-num new_line" data-linenumber="5" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.1.4</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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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<td class="diff-line-num new_line" data-linenumber="6" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Adapt watch file to also catch v$VERSION tarball names</span>
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<td class="diff-line-num new old_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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<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="plaintext"> * Clean up quilt patches</span>
</pre>
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<td class="diff-line-num 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">
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<td class="diff-line-num new_line" data-linenumber="8" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * Try to enable swig Python bindings</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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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<td class="diff-line-num new_line" data-linenumber="9" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> TODO: ... but failed</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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 26 Apr 2018 21:19:48</span> +0200</span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 03 Sep 2018 08:34:22</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">jellyfish (2.2.8-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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</li>
<li id="623e1fe488a7ff64fb7b06d083c94bb47d0555a6">
<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#623e1fe488a7ff64fb7b06d083c94bb47d0555a6"><strong>debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch</strong>
deleted
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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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<br>
</li>
<li id="dcf0532af16131e0f0d1f1b3d83276265b242593">
<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#dcf0532af16131e0f0d1f1b3d83276265b242593"><strong>debian/patches/add_small_mers.sh.patch</strong>
deleted
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1
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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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2
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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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3
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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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4
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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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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">---</span>
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7
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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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8
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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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9
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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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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"></span>
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11
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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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18
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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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<li id="76ce9724ed97a005df2dfe559d65dc1c62f53c3f">
<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#76ce9724ed97a005df2dfe559d65dc1c62f53c3f"><strong>debian/patches/drop-rpath</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Don't compile using an rpath</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Author: Michael R. Crusoe <crusoe@ucdavis.edu></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/python/setup.py</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/swig/python/setup.py</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -25,7 +25,6 @@</span></span>
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6
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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"> jf_libs = [re.sub(r'-l', '', x) for x in os.popen("pkg-config --libs-only-l jellyfish-2.0").read().rstrip().split()]</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> jf_libdir = [re.sub(r'-L', '', x) for x in os.popen("pkg-config --libs-only-L jellyfish-2.0").read().rstrip().split()]</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-jf_rpath = [re.sub(r'^', '-Wl,-rpath,', x) for x in jf_libdir]</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> jf_ldflags = os.popen("pkg-config --libs-only-other jellyfish-2.0").read().rstrip().split()</span>
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11
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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 class="gu" style="color: #800080; font-weight: 600;">@@ -35,7 +34,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> libraries = jf_libs,</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> library_dirs = jf_libdir,</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> extra_compile_args = ["-std=c++0x"] + jf_cflags,</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- extra_link_args = jf_ldflags + jf_rpath,</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;">+ extra_link_args = jf_ldflags,</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> language = "c++")</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> setup(name = 'dna_jellyfish',</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> version = '0.0.1',</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/Tuprules.tup</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;">+++ jellyfish/swig/Tuprules.tup</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -77,12 +77,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> JELLYFISH_LIBS = `pkg-config --libs jellyfish-2.0` </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ifdef JELLYFISH_RPATH</span></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;">- JELLYFISH_RPATH = @(JELLYFISH_RPATH)</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else</span></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;">- JELLYFISH_RPATH = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> ifdef RUBY_CFLAGS</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> RUBY_CFLAGS = @(RUBY_CFLAGS)</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/perl5/Makefile.PL</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/swig/perl5/Makefile.PL</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,7 +9,6 @@</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"> my $jf_cflags = `pkg-config --cflags jellyfish-2.0`;</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> my $jf_libs = `pkg-config --libs jellyfish-2.0`;</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $jf_rpath = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`;</span></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"> WriteMakefile(NAME => 'jellyfish',</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> CC => 'g++-4.4',</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;">--- jellyfish.orig/swig/perl5/Tupfile</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;">+++ jellyfish/swig/perl5/Tupfile</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> export PKG_CONFIG_PATH</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> SWIGFLAGS = -perl5</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> CXXFLAGS += $(JELLYFISH_CFLAGS) $(PERL_CFLAGS) -fPIC</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(PERL_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS += -shared $(JELLYFISH_LIBS) $(PERL_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx | jellyfish.pm <jf></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> : jellyfish_wrap.cxx |> !cxx |></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/python/Tupfile</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/swig/python/Tupfile</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> export PKG_CONFIG_PATH</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> SWIGFLAGS = -python</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> CXXFLAGS += $(JELLYFISH_CFLAGS) $(PYTHON_CFLAGS) -fPIC</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(PYTHON_LIBS)</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS += -shared $(JELLYFISH_LIBS) $(PYTHON_LIBS)</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx | jellyfish.py <jf></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> : jellyfish_wrap.cxx |> !cxx |></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/ruby/Tupfile</span></span>
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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;">+++ jellyfish/swig/ruby/Tupfile</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -3,7 +3,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"> export PKG_CONFIG_PATH</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> SWIGFLAGS = -ruby</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> CXXFLAGS += $(JELLYFISH_CFLAGS) $(RUBY_CFLAGS) -fPIC</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(RUBY_LIBS)</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+LDFLAGS += -shared $(JELLYFISH_LIBS) $(RUBY_LIBS)</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> : jellyfish_wrap.cxx |> !cxx |></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/ruby/extconf.rb</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/swig/ruby/extconf.rb</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7,6 +7,5 @@</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> $defs << `pkg-config --cflags jellyfish-2.0`.chomp << '-std=c++0x'</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> $libs << `pkg-config --libs jellyfish-2.0`.chomp</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$libs << `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`.chomp</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"> create_makefile('jellyfish')</span></pre>
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<li id="1cc4b89414889f6673c04af83da7a47f7be14f5a">
<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#1cc4b89414889f6673c04af83da7a47f7be14f5a"><strong>debian/patches/gcc-7.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Don't use -Werror</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> The SWIG-generated swig/perl5/swig_wrap.cpp gives warnings with</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> gcc 7, don't make these fatal with -Werror.</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff">Author: Adrian Bunk <bunk@debian.org></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">Last-Update: Tue, 15 Aug 2017 15:56:06 +0300</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/872262</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/development.mk</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/development.mk</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AM_CXXFLAGS += -Werror</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#AM_CXXFLAGS += -Werror</span></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"> # Count lines of code</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> .PHONY: cloc cloc_jellyfish</span></pre>
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<li id="87d775dfc70cd7349d92999c3cf4ecef0ce8e99f">
<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#87d775dfc70cd7349d92999c3cf4ecef0ce8e99f"><strong>debian/patches/modern-g++</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Use the version of g++ in Debian, not 4.4</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Author: Michael R. Crusoe <crusoe@ucdavis.edu></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/perl5/Makefile.PL</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/swig/perl5/Makefile.PL</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -11,8 +11,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> my $jf_libs = `pkg-config --libs jellyfish-2.0`;</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> WriteMakefile(NAME => 'jellyfish',</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;">- CC => 'g++-4.4',</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- LD => 'g++-4.4',</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CC => 'g++',</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ LD => 'g++',</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> CCFLAGS => "-std=c++0x $jf_cflags",</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> LIBS => "$jf_libs",</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> OBJECT => 'jellyfish_wrap.o',</span></pre>
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<li id="e29b151bd5860ac92a6c8994a6ea279159e34d37">
<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#e29b151bd5860ac92a6c8994a6ea279159e34d37"><strong>debian/patches/pkg-config-with-name</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: pkg-config must be called with package name</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Author: Michael R. Crusoe <crusoe@ucdavis.edu></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/swig/python/setup.py</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/swig/python/setup.py</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -21,7 +21,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> os.system("swig -c++ -python -o jellyfish_wrap.cxx ../jellyfish.i")</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> jf_include = [re.sub(r'-I', '', x) for x in os.popen("pkg-config --cflags-only-I jellyfish-2.0").read().rstrip().split()]</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;">-jf_cflags = os.popen("pkg-config --cflags-only-other").read().rstrip().split()</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;">+jf_cflags = os.popen("pkg-config --cflags-only-other jellyfish-2.0").read().rstrip().split()</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"> jf_libs = [re.sub(r'-l', '', x) for x in os.popen("pkg-config --libs-only-l jellyfish-2.0").read().rstrip().split()]</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> jf_libdir = [re.sub(r'-L', '', x) for x in os.popen("pkg-config --libs-only-L jellyfish-2.0").read().rstrip().split()]</span></pre>
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<a href="https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">manpage_whatis_entry.patch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># pkg-config-with-name</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># drop-rpath</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"># modern-g++</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"># spelling</span>
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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="LC2" class="line" lang="plaintext">reproducible.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">portability.patch</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/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Spelling fixes</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Author: Michael R. Crusoe <crusoe@ucdavis.edu></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- jellyfish.orig/doc/jellyfish.tex</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ jellyfish/doc/jellyfish.tex</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -140,7 +140,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> Important: the size of the couting field does NOT change the result,</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> it only impacts the amount of memory used. In particular, there is no</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> maximum value in the hash. Even if the counting field uses 5 bits, a</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;">-$k$-mer occuring 2 million times will have a value reported of 2</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;">+$k$-mer occurring 2 million times will have a value reported of 2</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> million (i.e., it is not capped at $2^5$).</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"> The \Opt{-c} specify the length (in bits) of the counting field. The</span></pre>
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