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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/ksw2">Debian Med / ksw2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/f42f8009e744386614f3782c967e1ac55e83c301">f42f8009</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-07-10T23:58:59+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">propagate HAVE_KALLOC with presence of kalloc.h
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ksw2/-/commit/da418f92e8e51907fc61ca1655f68db0dcdccc4b">da418f92</a></strong>
<div>
<span>by Etienne Mollier</span>
<i>at 2020-07-11T01:05:46+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">check and use parasail from /usr/include
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#6d5507768ac8975f221ead23baef90cb894ce802">
debian/patches/autoconf.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/1dff0e6b3018d1a26563c2e0666c97ac91df518d...da418f92e8e51907fc61ca1655f68db0dcdccc4b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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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"> autoconf-archive,</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"> pkg-config,</span>
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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"> zlib1g-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> libparasail-dev,</span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> libsimde-dev</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext">Standards-Version: 4.5.0</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">Vcs-Browser: https://salsa.debian.org/med-team/ksw2</span>
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<li id="6d5507768ac8975f221ead23baef90cb894ce802">
<a href="https://salsa.debian.org/med-team/ksw2/-/compare/1dff0e6b3018d1a26563c2e0666c97ac91df518d...da418f92e8e51907fc61ca1655f68db0dcdccc4b#6d5507768ac8975f221ead23baef90cb894ce802"><strong>debian/patches/autoconf.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@ Last-Update: Fri, 15 May 2020 11:45:35 +0200</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Provide automake build system to get proper library packaging</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- /dev/null</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/Makefile.am</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">ksw2</span>/Makefile.am</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -0,0 +1,19 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+lib_LTLIBRARIES = libksw2.la</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<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">@@ -25,7 +25,7 @@ Description: Provide automake build system to get proper library packaging</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">ksw2</span>/configure.ac</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="p">@@ -0,0 +1,66 @@</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# -*- Autoconf -*-</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;">+# Process this file with autoconf to produce a configure script.</span></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">@@ -80,11 +80,11 @@ Description: Provide automake build system to get proper library packaging</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Checks for header files.</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_HEADER_STDC</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_HEADERS([stdlib.h])</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_HEADERS([parasail.h],[AC_DEFINE([HAVE_PARASAIL], [1], [Use parasail])])</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" 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="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_PROG_MAKE_SET</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+dnl AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_HEADER([kalloc.h], [AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])] )</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CHECK_FILE([kalloc.h],[AC_DEFINE([HAVE_KALLOC], [1], [Use ksw2 own malloc functions])])</span></span>
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<pre style="margin: 0;"> <span id="LC88" 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="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+AC_CONFIG_FILES([</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Makefile</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" 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="94" 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">@@ -94,7 +94,7 @@ Description: Provide automake build system to get proper library packaging</td>
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<pre style="margin: 0;"> <span id="LC94" 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="LC95" 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="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/libksw2.pc.in</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">ksw2</span>/libksw2.pc.in</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"><span class="p">@@ -0,0 +1,12 @@</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+prefix=@prefix@</span></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+exec_prefix=${prefix}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,7 +108,7 @@ Description: Provide automake build system to get proper library packaging</td>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Libs: -L${libdir} -lksw2</span></span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Cflags: -I${includedir}</span></span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></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;">--- <span class="idiff left right">a</span>/Makefile</span></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;">--- <span class="idiff left right">ksw2.orig</span>/Makefile</span></span>
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112
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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;">+++ /dev/null</span></span>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="diff"><span class="p">@@ -1,58 +0,0 @@</span></span>
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114
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CC= gcc</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" 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="169" 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">@@ -169,3 +169,14 @@ Description: Provide automake build system to get proper library packaging</td>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_gg.o: ksw2.h</span></span>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_gg2.o: ksw2.h</span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ksw2_gg2_sse.o: ksw2.h</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ksw2.orig/cli.c</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ksw2/cli.c</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> #endif</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> </span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> #ifdef HAVE_PARASAIL</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "parasail.h"</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <parasail.h></span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> #endif</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> unsigned char seq_nt4_table[256] = {</span></pre>
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