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<h3>
Alexandre Mestiashvili pushed to branch master
at <a href="https://salsa.debian.org/med-team/gmap">Debian Med / gmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/commit/370503be162ea4c76bb4c0302ccb4cece58ed595">370503be</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-30T08:49:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch from upstream fixing FTBFS when a CPU has only SSE2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/commit/7f43693a2145acd36e3ebf4216616029e1ae1e0c">7f43693a</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-30T08:53:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Prepare for release
Gbp-Dch: Ignore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/commit/f80721f4d40286decb86d59813924f752462cb0d">f80721f4</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-31T09:37:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/commit/57f8b4ce9cfa484e108ac2c2cd1f06309c267db0">57f8b4ce</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-31T09:39:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix a typo in sse2 patch description
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/commit/ef2a4984ed09d9b66a7a02347085a92d21fbe32e">ef2a4984</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-31T09:40:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: XS-Autobuild: yes
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/commit/46f45d064d6df2eab450cb44fe37494aabd6ab39">46f45d06</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-31T09:41:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
Gbp-Dch: Ignore
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#10be0218bc9ad64897b060c1c8eb7f9cf37850e0">
<span class="new-file">
+
debian/patches/sse2.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gmap/compare/ecd23f0946f6dc8e838221407121f8544ad508f4...46f45d064d6df2eab450cb44fe37494aabd6ab39#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gmap (2018-07-04-3) unstable; urgency=medium</span>
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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"> * Bump Standards-Version to 4.2.1</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"> * Fix a typo in sse2 patch description</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * d/control: XS-Autobuild: yes</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> Fri, 31 Aug 2018 09:40:16 +0000</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">gmap (2018-07-04-2) unstable; urgency=medium</span>
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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 new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Add patch from upstream fixing FTBFS when a CPU has only SSE2</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Alexandre Mestiashvili <mestia@debian.org> Thu, 30 Aug 2018 08:51:09 +0000</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">gmap (2018-07-04-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/gmap/compare/ecd23f0946f6dc8e838221407121f8544ad508f4...46f45d064d6df2eab450cb44fe37494aabd6ab39#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,14 +4,14 @@ Uploaders: Shaun Jackman <sjackman@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Alexandre Mestiashvili <mestia@debian.org></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: non-free/science</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">XS-Autobuild: <span class="idiff left right">no</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">XS-Autobuild: <span class="idiff left right">yes</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Priority: optional</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh-exec,</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> help2man,</span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libbz2-dev,</span>
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<td class="diff-line-num old_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">
13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> zlib1g-dev</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.5</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/gmap</span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/gmap.git</span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://research-pub.gene.com/gmap</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/gmap/compare/ecd23f0946f6dc8e838221407121f8544ad508f4...46f45d064d6df2eab450cb44fe37494aabd6ab39#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sse2.patch</span>
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1
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<td class="diff-line-num new_line" data-linenumber="2" 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">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">only-do-cpuid-on-amd64-i386.patch</span>
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2
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<td class="diff-line-num new_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">
3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">install-data-local</span></pre>
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<a href="https://salsa.debian.org/med-team/gmap/compare/ecd23f0946f6dc8e838221407121f8544ad508f4...46f45d064d6df2eab450cb44fe37494aabd6ab39#10be0218bc9ad64897b060c1c8eb7f9cf37850e0"><strong>debian/patches/sse2.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Subject: Apply upstream patch fixing #902820</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> FTBFS on stretch/amd64 if CPU has SSE2 and nothing more</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">From: Thomas Wu <wu.thomas@gene.com></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Forwarded: Yes</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gmap.orig/src/extension-search.c</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ gmap/src/extension-search.c</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -340,13 +340,6 @@</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #endif</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-static void</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-print_vector_dec (__m128i x) {</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printf("%d %d %d %d\n",</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _mm_extract_epi32(x,0),_mm_extract_epi32(x,1),_mm_extract_epi32(x,2),_mm_extract_epi32(x,3));</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return;</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #if !defined(HAVE_SSE4_2)</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #define count_leading_zeroes_32(diff) ((diff >> 16) ? clz_table[diff >> 16] : 16 + clz_table[diff])</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- gmap.orig/src/kmer-search.c</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ gmap/src/kmer-search.c</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -215,7 +215,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> /* Algorithm 2: Stage3end_complete_path_run_gmap: complete_path -> hits */</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </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;">-#ifdef HAVE_SSE2</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef DEBUG8</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef HAVE_SSE4_1</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> static void</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> print_vector_dec (__m128i x) {</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> printf("%d %d %d %d\n",</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -223,6 +224,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> return;</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </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"> #if !defined(HAVE_SSE4_2)</span></pre>
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