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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/abyss">Debian Med / abyss</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/6318aea715c951f6ea12423cb1ba151a2624c81a">6318aea7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-14T20:55:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace python-markdown by markdown
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/d4f29a51139652335b672b040da9255476cf6500">d4f29a51</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-14T20:55:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/af46cd7e8caca2f36b1430d6b30c1e0e542d948c">af46cd7e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-14T20:55:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove patches abyss-32-bit.patch, gtest.patch that are missing from debian/patches/series.
Fixes lintian: patch-file-present-but-not-mentioned-in-series
See https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/cc6e90d1a3e8a038e6e13ac390e0b1acd328c196">cc6e90d1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-14T20:55:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Repository, Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/e529ea45ff41d533178d02e9b9647be0ada89b21">e529ea45</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-14T20:55:44Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete fields Contact, Name from debian/upstream/metadata.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/e0effa0ecfe7826b9146b7a600bdf13d925e39fb">e0effa0e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-14T23:00:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use libtext-multimarkdown-perl to obtain html documentation
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/abyss/commit/c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb">c0bbb786</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-14T23:11:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#8e58444b4b5ce26cf2d1a8755ae3a96f179592ec">
<span class="deleted-file">
−
debian/patches/abyss-32-bit.patch
</span>
</a>
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<li class="file-stats">
<a href="#6b6b5226a5cdc83527e5cc2a028b21d28a7ace1c">
<span class="deleted-file">
−
debian/patches/gtest.patch
</span>
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb#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">abyss (2.2.3-2) 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 libtext-multimarkdown-perl to obtain html documentation</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: #942908</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"> * Standards-Version: 4.4.1</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"></span>
</pre>
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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"> -- Andreas Tille <tille@debian.org> Sun, 15 Dec 2019 00:00:48 +0100</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"></span>
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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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">abyss (2.2.3-1) unstable; urgency=medium</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"></span>
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<td class="diff-line-num old_line" data-linenumber="3" 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="11" 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="LC11" class="line" lang="plaintext"> * New upstream version</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,6 @@ Uploaders: Andreas Tille <tille@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<td class="diff-line-num new_line old" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> python-markdown,</span>
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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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libboost-graph-dev,</span>
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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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libopenmpi-dev,</span>
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<td class="diff-line-num old_line" data-linenumber="11" 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="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"> libsparsehash-dev,</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">@@ -13,7 +12,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libsqlite3-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> help2man</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/abyss</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/abyss.git</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss</span>
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<li id="8e58444b4b5ce26cf2d1a8755ae3a96f179592ec">
<a href="https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb#8e58444b4b5ce26cf2d1a8755ae3a96f179592ec"><strong>debian/patches/abyss-32-bit.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Graham Inggs <graham@nerve.org.za></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Thu, 16 Jul 2015 10:44:56 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/bcgsc/abyss/pull/278</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Bug-Debian: http://bugs.debian.org/780409</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Description: Fix FTBFS on 32-bit architectures</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> Version 1.5.2-1 of abyss FTBFS on 32-bit architectures (armhf, i386 and</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> powerpc). Previous versions built fine on all architectures.</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"> There were a couple of places in the code that was introduced in version</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> 1.5.2 where size_t data type was used instead of a fixed size data type.</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> The patch builds on amd64, i386 and armhf with and all unit tests passed.</span>
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12
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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"> Question: is this software useful on a 32-bit system at all?</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff">--- a/Common/StringUtil.h</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Common/StringUtil.h</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="p">@@ -178,7 +178,7 @@</span> bool isReadNamePair(const std::string& n</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> return false;</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static inline size_t SIToBytes(std::istringstream& iss)</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;">+static inline unsigned long long SIToBytes(std::istringstream& iss)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> double size;</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> std::string units;</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -194,7 +194,7 @@</span> static inline size_t SIToBytes(std::istr</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> // no units given; clear fail flag</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> // and assume bytes</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> iss.clear(std::ios::eofbit);</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;">- return (size_t)ceil(size);</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return (unsigned long long)ceil(size);</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> if (units.size() > 1) {</span></pre>
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<a href="https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb#6b6b5226a5cdc83527e5cc2a028b21d28a7ace1c"><strong>debian/patches/gtest.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Anthony Raymond <traymond@bcgsc.ca></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Updated: Wed, 17 Sep 2014 12:17:23 -0700</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Make sure gtest works properly</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> I had to follow the instructions on this post to build libgtest.a and libgtest_main.a:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> http://askubuntu.com/questions/145887/why-no-library-files-installed-for-google-test</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"> Attention: This patch needs heave adaption and is deactivated for the moment</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">--- a/Unittest/Makefile.am</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;">+++ b/Unittest/Makefile.am</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -1,58 +1,72 @@</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;">+check_LIBRARIES = libgtest.a libgtest_main.a</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;">+</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+gtest-all.cc:</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;">+ cp $(GTEST)/src/gtest-all.cc .</span></span>
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<pre style="margin: 0;">-<span id="LC16" 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="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+gtest_main.cc:</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;">+ cp $(GTEST)/src/gtest_main.cc .</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libgtest_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libgtest_a_SOURCES = gtest-all.cc</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libgtest_main_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+libgtest_main_a_SOURCES = gtest_main.cc gtest-all.cc</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> UNIT_TESTS = common_stringutil</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> check_PROGRAMS = common_stringutil</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> common_stringutil_SOURCES = Common/StringUtilTest.cpp</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> common_stringutil_CPPFLAGS = -I$(top_srcdir)</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;">-common_stringutil_LDADD = $(GTEST_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+common_stringutil_LDADD = libgtest_main.a $(GTEST_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> UNIT_TESTS += common_histogram</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> check_PROGRAMS += common_histogram</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> common_histogram_SOURCES = Common/HistogramTest.cpp</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> common_histogram_CPPFLAGS = -I$(top_srcdir)</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;">-common_histogram_LDADD = $(GTEST_LIBS)</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;">+common_histogram_LDADD = libgtest_main.a $(GTEST_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> UNIT_TESTS += common_bitutil</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"> check_PROGRAMS += common_bitutil</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> common_bitutil_SOURCES = Common/BitUtilTest.cpp</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> common_bitutil_CPPFLAGS = -I$(top_srcdir)</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-common_bitutil_LDADD = $(GTEST_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+common_bitutil_LDADD = libgtest_main.a $(GTEST_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> UNIT_TESTS += common_kmer</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> check_PROGRAMS += common_kmer</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> common_kmer_SOURCES = Common/KmerTest.cpp</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> common_kmer_CPPFLAGS = -I$(top_srcdir)</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-common_kmer_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+common_kmer_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> UNIT_TESTS += common_sequence</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> check_PROGRAMS += common_sequence</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> common_sequence_SOURCES = Common/Sequence.cc</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> common_sequence_CPPFLAGS = -I$(top_srcdir)</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;">-common_sequence_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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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;">+common_sequence_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> </span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> UNIT_TESTS += common_KmerIterator</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> check_PROGRAMS += common_KmerIterator</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"> common_KmerIterator_SOURCES = Common/KmerIteratorTest.cpp</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> common_KmerIterator_CPPFLAGS = -I$(top_srcdir)</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> </span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> UNIT_TESTS += common_sam</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> check_PROGRAMS += common_sam</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> common_sam_SOURCES = Common/SAM.cc</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> common_sam_CPPFLAGS = -I$(top_srcdir)</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-common_sam_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+common_sam_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> </span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> UNIT_TESTS += BloomFilter</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"> check_PROGRAMS += BloomFilter</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"> BloomFilter_SOURCES = Konnector/BloomFilter.cc</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> BloomFilter_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> BloomFilter_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)</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;">-BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</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;">+BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"> </span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"> UNIT_TESTS += Konnector_DBGBloom</span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> check_PROGRAMS += Konnector_DBGBloom</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> Konnector_DBGBloom_SOURCES = Konnector/DBGBloomTest.cpp</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> Konnector_DBGBloom_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"> Konnector_DBGBloom_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"> UNIT_TESTS += Konnector_DBGBloomAlgorithms</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"> check_PROGRAMS += Konnector_DBGBloomAlgorithms</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="p">@@ -61,38 +75,38 @@</span> Konnector_DBGBloomAlgorithms_CPPFLAGS =</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"> Konnector_DBGBloomAlgorithms_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"> Konnector_DBGBloomAlgorithms_LDADD = \</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"> $(top_builddir)/Common/libcommon.a \</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(GTEST_LIBS)</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ libgtest_main.a $(GTEST_LIBS)</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"> UNIT_TESTS += graph_ConstrainedBFSVisitor</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"> check_PROGRAMS += graph_ConstrainedBFSVisitor</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"> graph_ConstrainedBFSVisitor_SOURCES = Graph/ConstrainedBFSVisitorTest.cpp</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"> graph_ConstrainedBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common</span>
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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;">-graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="105" 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">
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;">+graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"> UNIT_TESTS += graph_BidirectionalBFS</span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"> check_PROGRAMS += graph_BidirectionalBFS</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"> graph_BidirectionalBFS_SOURCES = Graph/BidirectionalBFSTest.cpp</span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"> graph_BidirectionalBFS_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"> </span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"> UNIT_TESTS += graph_AllPathsSearch</span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"> check_PROGRAMS += graph_AllPathsSearch</span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"> graph_AllPathsSearch_SOURCES = Graph/AllPathsSearchTest.cpp</span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"> graph_AllPathsSearch_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common</span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"> </span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"> UNIT_TESTS += graph_HashGraph</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"> check_PROGRAMS += graph_HashGraph</span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"> graph_HashGraph_SOURCES = Graph/HashGraphTest.cpp</span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"> graph_HashGraph_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common</span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"> </span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"> UNIT_TESTS += graph_ConstrainedBidiBFSVisitor</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"> check_PROGRAMS += graph_ConstrainedBidiBFSVisitor</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"> graph_ConstrainedBidiBFSVisitor_SOURCES = \</span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"> Graph/ConstrainedBidiBFSVisitorTest.cpp</span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"> graph_ConstrainedBidiBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common</span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"> </span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"> UNIT_TESTS += Konnector_konnector</span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"> check_PROGRAMS += Konnector_konnector</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="p">@@ -102,7 +116,7 @@</span> Konnector_konnector_CPPFLAGS = -I$(top_s</span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"> Konnector_konnector_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)</span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"> Konnector_konnector_LDADD = \</span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"> $(top_builddir)/Align/libalign.a \</span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"> </span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"> ##Tests for log kmer counting / Counting bloom filter</span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"> </span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/configure.ac</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/configure.ac</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="p">@@ -89,10 +89,12 @@</span> fi</span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"> # GTest</span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"> AC_ARG_WITH(gtest, AS_HELP_STRING([--with-gtest=PATH],</span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"> [specify prefix directory for the installed gtest library]))</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+gtest_src="/usr/src/gtest"</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"> if test "$with_gtest" -a -d "$with_gtest"; then</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"> gtest_cppflags="-I$with_gtest/include"</span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- gtest_ldflags="-L$with_gtest/lib"</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ gtest_src="$with_gtest"</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_SUBST(GTEST, "$gtest_src")</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"> AC_ARG_ENABLE(mpich, AS_HELP_STRING([--enable-mpich],</span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"> [use MPICH (default is to use Open MPI)]))</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="p">@@ -118,7 +120,7 @@</span> boost_ver=1.55.0</span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"> boost_ver_dir=boost_1_55_0</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"> AC_SUBST(CPPFLAGS,</span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"> "-I$my_abs_srcdir $boost_cppflags $mpi_cppflags $gtest_cppflags $CPPFLAGS -isystem$my_abs_srcdir/$boost_ver_dir")</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_SUBST(LDFLAGS, "$mpi_ldflags $gtest_ldflags $LDFLAGS")</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_SUBST(LDFLAGS, "$mpi_ldflags $LDFLAGS")</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"> # Check for the MPI parallel computing library.</span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"> libs="$LIBS"</span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="p">@@ -194,8 +196,7 @@</span> fi</span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"> libs="$LIBS"</span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"> AC_CHECK_HEADERS([gtest/gtest.h])</span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"> AC_CHECK_LIB([pthread], [pthread_create])</span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AC_CHECK_LIB([gtest_main],[main])</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes -a $ac_cv_lib_gtest_main_main = yes])</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes])</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"> AC_SUBST(GTEST_LIBS, "$LIBS")</span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"> LIBS=$libs</span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -15,7 +15,7 @@ override_dh_auto_configure:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> markdown<span class="idiff left right">_py -f README.html README.md</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> markdown<span class="idiff left right"> README.md > README.html</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> dh_auto_install --destdir=debian/tmp</span>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Name: ABySS</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> Author: ></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> and Steven J.M. Jones and İnanç Birol</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> Title: "ABySS: A parallel assembler for short read sequence data"</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Journal: Genome Research</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> Year: 2009</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Volume: 19</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Number: 6</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> Pages: 1117-23</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> PMID: 19251739</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> DOI: 10.1101/gr.089532.108</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> URL: http://genome.cshlp.org/content/19/6/1117</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> <span class="idiff left right"> </span>Author: ></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right"> </span>Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <span class="idiff left right"> </span>and Steven J.M. Jones and İnanç Birol</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <span class="idiff left right"> </span>Title: "ABySS: A parallel assembler for short read sequence data"</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <span class="idiff left right"> </span>Journal: Genome Research</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <span class="idiff left right"> </span>Year: 2009</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>Volume: 19</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>Number: 6</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>Pages: 1117-23</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>PMID: 19251739</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> </span>DOI: 10.1101/gr.089532.108</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <span class="idiff left right"> </span>URL: http://genome.cshlp.org/content/19/6/1117</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <span class="idiff left right"> </span>eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html</span>
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<td class="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="plaintext">Registry:</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> - Name: bio.tools</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> Entry: ABySS</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> - Name: OMICtools</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> Entry: OMICS_00006</span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext"> - Name: SciCrunch</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> Entry: SCR_010709</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> Entry: abyss</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Contact: Shaun Jackman <sjackman@gmail.com></span></pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Name: bio.tools</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Entry: ABySS</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">- Name: OMICtools</span>
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<td class="diff-line-num new old_line" data-linenumber="26" 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="LC19" class="line" lang="plaintext"> Entry: OMICS_00006</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Entry: SCR_010709</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> Entry: abyss</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Repository: https://github.com/bcgsc/abyss.git</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Repository-Browse: https://github.com/bcgsc/abyss</span></pre>
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