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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/salmon">Debian Med / salmon</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e">eea6c1a3</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-12-13T15:30:33Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Take over patches from previous version if applicable.  Keep some for documentation purpose

</pre>

</li>

</ul>

<h4>6 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#40349202e4aa955a6a71882e02d308dd6cc8cedd">

<span class="new-file">

+

debian/patches/0008-Remove-salmon_core-lib.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#64aced6e03dbb6e07f24819ae33fbe4458991d23">

<span class="new-file">

+

debian/patches/add_MEM_F_SELF_OVLP.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bae08dca7af50ae6494331a147cd30150ecb5714">

<span class="new-file">

+

debian/patches/disable-version-check.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#2c5169d8f75b7c6f4db2798448154c0c3c31d73a">

<span class="new-file">

+

debian/patches/use-system-pkg-config-tbb.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="40349202e4aa955a6a71882e02d308dd6cc8cedd">

<a href="https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e#40349202e4aa955a6a71882e02d308dd6cc8cedd"><strong>debian/patches/0008-Remove-salmon_core-lib.patch</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From: Kevin Murray <spam@kdmurray.id.au></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Date: Sat, 30 Jan 2016 18:06:52 +0200</span>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Subject: Remove salmon_core lib</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Remark: This patch is deactivated</span>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> Upstream code has changed a lot and it is not documented why</span>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> salmon_core lib was removed.  Before breaking anything the</span>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> hopefully harmles lib is created as upstream seems to consider</span>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> sensible.</span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff">---</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> src/CMakeLists.txt | 8 ++------</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> 1 file changed, 2 insertions(+), 6 deletions(-)</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/CMakeLists.txt</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/src/CMakeLists.txt</span></span>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -102,9 +102,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff">   set(CMAKE_INSTALL_RPATH_USE_LINK_PATH FALSE)</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> endif()</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 class="gd" style="color: #000; background-color: #fdd;">-# Build the Salmon library</span></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;">-add_library(salmon_core ${SALMON_LIB_SRCS} )</span></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;">-</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"> # Build the salmon executable</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -124,7 +121,6 @@</span></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"> # Link the executable</span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> target_link_libraries(salmon</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;">-    salmon_core</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff">     gff</span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff">     ${PTHREAD_LIB}</span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff">     ${Boost_LIBRARIES}</span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -146,42 +142,41 @@</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> # External dependencies of salmon_core and salmon</span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> ##</span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> if (${FETCHED_JEMALLOC})</span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-   add_dependencies(salmon_core libjemalloc)</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #   add_dependencies(salmon_core libjemalloc)</span></span>

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40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">    add_dependencies(salmon libjemalloc)</span>

</pre>

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41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> endif()</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="42" 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">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="43" 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">

43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> if (${FETCHED_BOOST})</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="44" 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">

44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-   add_dependencies(salmon_core libboost)</span></span>

</pre>

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45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    # add_dependencies(salmon_core libboost)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff">    add_dependencies(salmon libboost)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="47" 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">

47

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> endif()</span>

</pre>

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48

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>

</pre>

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49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> if (${FETCHED_JELLYFISH})</span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-   add_dependencies(salmon_core libjellyfish)</span></span>

</pre>

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51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #add_dependencies(salmon_core libjellyfish)</span></span>

</pre>

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52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">    add_dependencies(salmon libjellyfish)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="53" 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">

53

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> endif()</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> if (${FETCHED_TBB})</span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-   add_dependencies(salmon_core libtbb)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #add_dependencies(salmon_core libtbb)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff">    add_dependencies(salmon libtbb)</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> endif()</span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_dependencies(salmon_core libcereal)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#add_dependencies(salmon_core libcereal)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> add_dependencies(salmon libcereal)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_dependencies(salmon_core libstadenio)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#add_dependencies(salmon_core libstadenio)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> add_dependencies(salmon libstadenio)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_dependencies(salmon_core libspdlog)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#add_dependencies(salmon_core libspdlog)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> add_dependencies(salmon libspdlog)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> ## FIXME: This was commented in version 0.7.2 in a quilt patch</span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_dependencies(salmon_core libbwa)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#add_dependencies(salmon_core libbwa)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> add_dependencies(salmon libbwa)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_dependencies(salmon_core libgff)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#add_dependencies(salmon_core libgff)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> add_dependencies(salmon libgff)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_dependencies(salmon_core libdivsufsort)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#add_dependencies(salmon_core libdivsufsort)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> add_dependencies(salmon libdivsufsort)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>

</pre>

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81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> # Link the executable</span>

</pre>

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82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> target_link_libraries(unitTests</span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    salmon_core</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff">     gff</span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff">     ${PTHREAD_LIB}</span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff">     ${Boost_LIBRARIES}</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -259,7 +254,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> # install(FILES ${Boost_LIBRARIES}</span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> #                   DESTINATION ${INSTALL_LIB_DIR})</span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-install(TARGETS salmon salmon_core</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+install(TARGETS salmon</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">                 RUNTIME DESTINATION bin</span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff">                 LIBRARY DESTINATION lib</span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff">                 ARCHIVE DESTINATION lib</span></pre>

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<br>

</li>

<li id="64aced6e03dbb6e07f24819ae33fbe4458991d23">

<a href="https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e#64aced6e03dbb6e07f24819ae33fbe4458991d23"><strong>debian/patches/add_MEM_F_SELF_OVLP.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: redefine MEM_F_SELF_OVLP</span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> libbwa upstream has dropped MEM_F_SELF_OVLP in their commit </span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> 1247dc234668c1d7357fa6343222e9b5730e832d. This patch re-introduces this</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> definition to fix an FTBFS.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Remark: This patch is deactivated since current source code</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> builds nicely without it.</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Author: Sascha Steinbiss <sascha@steinbiss.name></span>

</pre>

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8

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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/src/SalmonQuantify.cpp</span></span>

</pre>

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9

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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/src/SalmonQuantify.cpp</span></span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -54,6 +54,7 @@ extern "C" {</span></span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> #include "ksort.h"</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> #include "kvec.h"</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #include "utils.h"</span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define MEM_F_SELF_OVLP 0x40</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> }</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> // Jellyfish 2 include</span>

</pre>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -126,6 +127,7 @@ extern "C" {</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #include "RapMapUtils.hpp"</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> //#include "TextBootstrapWriter.hpp"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> /****** QUASI MAPPING DECLARATIONS *********/</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> using MateStatus = rapmap::utils::MateStatus;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> using QuasiAlignment = rapmap::utils::QuasiAlignment;</span></pre>

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<br>

</li>

<li id="bae08dca7af50ae6494331a147cd30150ecb5714">

<a href="https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e#bae08dca7af50ae6494331a147cd30150ecb5714"><strong>debian/patches/disable-version-check.patch</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Michael R. Crusoe <crusoe@ucdavis.edu></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: Disable the newer version check</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;">--- a/src/Salmon.cpp</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;">+++ b/src/Salmon.cpp</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;">@@ -208,10 +208,10 @@ int main(int argc, char* argv[]) {</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">       std::exit(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"> </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;">-    if (!vm.count("no-version-check")) {</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;">-      std::string versionMessage = getVersionMessage();</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;">-      std::cout << versionMessage;</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;">-    }</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;">+    //if (!vm.count("no-version-check")) {</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;">+    //  std::string versionMessage = getVersionMessage();</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;">+    //  std::cout << versionMessage;</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>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">     // po::notify(vm);</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_libs.patch</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">disable-version-check.patch</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># use-system-pkg-config-tbb.patch</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># 0008-Remove-salmon_core-lib.patch</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># add_MEM_F_SELF_OVLP.patch</span></pre>

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</table>

<br>

</li>

<li id="2c5169d8f75b7c6f4db2798448154c0c3c31d73a">

<a href="https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e#2c5169d8f75b7c6f4db2798448154c0c3c31d73a"><strong>debian/patches/use-system-pkg-config-tbb.patch</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Use pkgconfig to find the system library for tbb</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Remark: This patch is deactivated for the moment.</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">        use_debian_packaged_libs.patch is able to detect tbb</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">        and there is no point to fiddle around now any more.</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">        However, may be this is more elegant and the patch is</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">        left as documentation.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Author: Michael R. Crusoe <crusoe@ucdavis.edu></span>

</pre>

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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/CMakeLists.txt</span></span>

</pre>

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9

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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/CMakeLists.txt</span></span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -287,6 +287,9 @@ endif()</span></span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> set(Boost_USE_MULTITHREADED ON)</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> #set(Boost_USE_STATIC_RUNTIME OFF)</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+find_package (PkgConfig)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pkg_check_modules(TBB REQUIRED tbb)</span></span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> find_package(ZLIB)</span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> if(NOT ZLIB_FOUND)</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">   message(FATAL_ERROR "zlib must be installed before configuration & building can proceed")</span></pre>

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<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/salmon/commit/eea6c1a38ffac3dd8dded8144582ff61ff6a587e#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="25" 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">@@ -25,6 +25,9 @@ CMAKE_EXTRA_FLAGS += -DDEBIAN_BUILD=1 \</td>

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25

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25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">     dh $@ --with sphinxdoc</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

26

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<td class="diff-line-num new_line" data-linenumber="26" 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">

26

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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">

27

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27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">override_dh_auto_configure:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">     # See here</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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="29" 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="LC29" class="line" lang="plaintext">     #    https://github.com/COMBINE-lab/salmon/issues/87</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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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30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">     # for a discussion with upstream why it is necessary to include rapmap source</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_line" data-linenumber="31" 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">

31

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">     mkdir -p $(CURDIR)/external/install/src/rapmap</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" 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">

29

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<td class="diff-line-num new_line" data-linenumber="32" 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="LC32" class="line" lang="plaintext">     cp -av /usr/share/rapmap/src/* $(CURDIR)/external/install/src/rapmap</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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">

30

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<td class="diff-line-num new_line" data-linenumber="33" 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">

33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">     dh_auto_configure -- $(CMAKE_EXTRA_FLAGS)</span>

</pre>

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