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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/9df87b4f3323daec588377fa3e909f1cd77e7ae5">9df87b4f</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-23T18:16:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">build anywhere using libsimde-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/dcb81eb097e582b30f9c2c699447a31d1769c079">dcb81eb0</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-23T18:16:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Mark mmseqs2-examples as Multi-Arch: foreign
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/214c58127b912595d58163d9e826250e85da8ee0">214c5812</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-23T18:16:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up debian/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/b0a840aa7e4f91a1afe37909d19fe23956d5449c">b0a840aa</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-23T18:16:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/upstream/metadata: add GitHub related fields
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1a0453e516e167132f0f9392c87de0ea5fe79145">
<span class="new-file">
+
debian/bin/simd-dispatch
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#e6ea635754248ef19ddbf9613e6c62a5311ac353">
debian/mmseqs2.install
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<span class="new-file">
+
debian/patches/simde
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1a0453e516e167132f0f9392c87de0ea5fe79145">
<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#1a0453e516e167132f0f9392c87de0ea5fe79145"><strong>debian/bin/simd-dispatch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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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="shell"><span class="nv" style="color: #008080;">BASE</span><span class="o" style="font-weight: 600;">=</span>/usr/bin/mmseqs</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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>test_and_run <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> /proc/cpuinfo <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "${cmd}" "$@"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">cmd</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></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="shell"> <span class="nb" style="color: #0086b3;">exit</span></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="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>SIMD <span class="k" style="font-weight: 600;">in </span>avx2 avx sse4.1 ssse3 sse3 sse2 sse mmx <span class="p">;</span> <span class="k" style="font-weight: 600;">do </span>test_and_run <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SIMD</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fallback to plain option</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;">$BASE</span><span class="nt" style="color: #000080;">-plain</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mmseqs2 (10-6d92c+ds-3) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Enable building on non-X86 and with less than SSE4.1 using</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> libsimde-dev</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Mark mmseqs2-examples as Multi-Arch: foreign</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Clean up debian/copyright</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * debian/upstream/metadata: add GitHub related fields</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Thu, 23 Apr 2020 16:39:36 +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">mmseqs2 (10-6d92c+ds-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#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">@@ -8,14 +8,16 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libgzstream-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libzstd-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> libbz2-dev</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> libbz2-dev,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libsimde-dev</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mmseqs2.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/soedinglab/MMseqs2</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Package: mmseqs2</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Architecture: amd64 kfreebsd-amd64</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Architecture: any</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Built-Using: ${simde:Built-Using}</span>
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19
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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20
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${misc:Depends}</span>
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<td class="diff-line-num new_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">Description: ultra fast and sensitive protein search and clustering</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,6 +32,7 @@ Description: ultra fast and sensitive protein search and clustering</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Package: mmseqs2-examples</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Multi-Arch: foreign</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">Recommends: mmseqs2</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Description: optional resources for the mmseqs2 package</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -10,11 +10,6 @@ Files: *</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Copyright: 2012 The MMseqs Development Team</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">License: GPL-3</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">Files: debian/missing-sources/userguide/eisvogel.tex</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Copyright: 2014-2019 John MacFarlane</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> 2017-2019 Pascal Wagler</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Files: src/alignment/DistanceCalculator.h</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> src/alignment/StripedSmithWaterman.cpp</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> src/alignment/StripedSmithWaterman.h</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">@@ -77,19 +72,10 @@ Files: lib/cacode/*</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">Copyright: 2008 Michiaki Hamada</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">Files: lib/kseq/kseq_buffer_reader.h</span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">Copyright: 2016 Milot Mirdita</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">License: Expat</span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">Files:</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> lib/ksw2/kseq.h</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> lib/kseq/kseq.h</span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">Copyright: 2009 Attractive Chaos <attractor@live.co.uk></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">License: Expat</span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">Files: lib/ksw2/*</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">Copyright: 2018 Dana-Farber Cancer Institute</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> 2017-2018 Broad Institute Inc.</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> 2009 Attractive Chaos <attractor@live.co.uk></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">License: Expat</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">Files: lib/omptl/*</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">@@ -104,6 +90,11 @@ Files: debian/*</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">Copyright: 2019 Shayan Doust <hello@shayandoust.me></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">License: GPL-3</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">Files: debian/missing-sources/userguide/eisvogel.tex</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">Copyright: 2014-2019 John MacFarlane</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> 2017-2019 Pascal Wagler</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">License: CC0-1.0</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> CC0 1.0 Universal</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> .</span>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#e6ea635754248ef19ddbf9613e6c62a5311ac353"><strong>debian/mmseqs2.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">util</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bash</span><span class="o" style="font-weight: 600;">-</span><span class="nx">completion</span><span class="o" style="font-weight: 600;">.</span><span class="nx">sh</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">README</span><span class="o" style="font-weight: 600;">.</span><span class="nx">md</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">missing</span><span class="o" style="font-weight: 600;">-</span><span class="nx">sources</span><span class="o" style="font-weight: 600;">/</span><span class="nx">userguide</span><span class="o" style="font-weight: 600;">/</span><span class="nx">userguide</span><span class="o" style="font-weight: 600;">.</span><span class="nx">pdf</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs2</span></span></pre>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">mmseqs</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -2,3 +2,4 @@ fix_tests.patch</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">fix_util_installation.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_system_zstd.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">use_system_gzstream.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">simde</span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Enable building on non-x86 and less than SSE4.1</span></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;">--- mmseqs2.orig/src/CMakeLists.txt</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;">+++ mmseqs2/src/CMakeLists.txt</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -128,21 +128,6 @@</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> append_target_property(mmseqs-framework LINK_FLAGS -msse4.1)</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> elseif (HAVE_NEON)</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> target_compile_definitions(mmseqs-framework PUBLIC -DSSE=1 -DNEON=1)</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-else ()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- include(CheckSSEFeatures)</span></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">
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;">- append_target_property(mmseqs-framework COMPILE_FLAGS ${SSE_FLAGS})</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;">- append_target_property(mmseqs-framework LINK_FLAGS ${SSE_FLAGS})</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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">
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;">- if (HAVE_AVX2_EXTENSIONS)</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;">- target_compile_definitions(mmseqs-framework PUBLIC -DAVX2=1)</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;">- # debugging</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;">- # list(APPEND MMSEQS_DEFINITIONS -DSSE=1)</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;">- else ()</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (HAVE_SSE4_1_EXTENSIONS)</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- target_compile_definitions(mmseqs-framework PUBLIC -DSSE=1)</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- else ()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
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;">- message(FATAL_ERROR "At least SSE4.2 is needed to compile!")</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- endif (HAVE_SSE4_1_EXTENSIONS)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- endif (HAVE_AVX2_EXTENSIONS)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> endif ()</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"> # tinyexpr</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -252,10 +237,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> add_subdirectory(version)</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> set(mmseqs_source_files mmseqs.cpp)</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- add_executable(mmseqs ${mmseqs_source_files})</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- mmseqs_setup_derived_target(mmseqs)</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- target_link_libraries(mmseqs version)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- install(TARGETS mmseqs DESTINATION bin)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ add_executable(mmseqs${EXE_SUFFIX} ${mmseqs_source_files})</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ mmseqs_setup_derived_target(mmseqs${EXE_SUFFIX})</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ target_link_libraries(mmseqs${EXE_SUFFIX} version)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ install(TARGETS mmseqs${EXE_SUFFIX} DESTINATION bin)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> if (HAVE_TESTS)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> add_subdirectory(test)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/lib/simd/simd.h</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/lib/simd/simd.h</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -50,11 +50,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> #define SSE</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "sse2neon.h"</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <xmmintrin.h></span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse.h></span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> #ifdef AVX512</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> #include <zmmintrin.h.h> // AVX512</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -284,11 +281,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> #endif //AVX_SUPPORT</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef SSE</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse4.1.h></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> uint16_t simd_hmax16(const __m128i buffer);</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> uint8_t simd_hmax8(const __m128i buffer);</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifndef NEON</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h> //SSE4.1</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> // double support</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> #ifndef SIMD_DOUBLE</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> #define SIMD_DOUBLE</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="p">@@ -311,7 +306,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> #define simdf64_andnot(x,y) _mm_andnot_pd(x,y)</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> #define simdf64_xor(x,y) _mm_xor_pd(x,y)</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> #endif //SIMD_DOUBLE</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> // float support</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> #ifndef SIMD_FLOAT</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -395,7 +389,6 @@</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> #define simdi32_i2f(x) _mm_cvtepi32_ps(x) // convert integer to s.p. float</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> #define simdi_i2fcast(x) _mm_castsi128_ps(x)</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> #endif //SIMD_INT</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif //SSE</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> </span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> #ifdef NEON</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> inline uint16_t simd_hmax16(const __m128i buffer) {</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="p">@@ -488,7 +481,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> return 0;</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> }</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> #else</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef SSE</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> inline unsigned short extract_epi16(__m128i v, int pos) {</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> switch(pos){</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> case 0: return _mm_extract_epi16(v, 0);</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -503,7 +495,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> return 0;</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> }</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> /* horizontal max */</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -608,7 +599,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> //</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> //TODO fix this</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef SSE</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> float __attribute__((aligned(16))) res;</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> __m128 P; // query 128bit SSE2 register holding 4 floats</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> __m128 R;// result</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="p">@@ -637,7 +627,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> R = _mm_add_ps(R,P);</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> _mm_store_ss(&res, R);</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> return res;</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> //#endif</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> return tj[0] * qi[0] + tj[1] * qi[1] + tj[2] * qi[2] + tj[3] * qi[3]</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> + tj[4] * qi[4] + tj[5] * qi[5] + tj[6] * qi[6] + tj[7] * qi[7]</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/itoa.h</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/itoa.h</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -25,7 +25,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> #ifdef NEON</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> #include "sse2neon.h"</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> #else</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse2.h></span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> #include <stdint.h></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/CMakeLists.txt</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/CMakeLists.txt</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -8,6 +8,7 @@</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> set(HAVE_SANITIZER 0 CACHE BOOL "Have Sanitizers")</span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> set(INSTALL_UTIL 1 CACHE BOOL "Install util scripts")</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> set(VERSION_OVERRIDE "" CACHE STRING "Override version string in help and usage messages")</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(EXE_SUFFIX "" CACHE STRING "Suffix to add to executable names")</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> #Sanitizers</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> if (${HAVE_SANITIZER})</span>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -40,9 +41,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> # set flags</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> set(MMSEQS_CXX_FLAGS "-std=c++0x")</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if (NOT ${HAVE_NEON})</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- set(MMSEQS_CXX_FLAGS "${MMSEQS_CXX_FLAGS} -m64")</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-endif ()</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> # Compiler-specific features</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> if (CMAKE_COMPILER_IS_CLANG)</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/prefiltering/UngappedAlignment.cpp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/prefiltering/UngappedAlignment.cpp</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="p">@@ -71,12 +71,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> simd_int vscore = simdi_setzero();</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> simd_int vMaxScore = simdi_setzero();</span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> const simd_int vBias = simdi8_set(bias);</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifndef AVX2</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- #ifdef SSE</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> const simd_int sixten = simdi8_set(16);</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> const simd_int fiveten = simdi8_set(15);</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> for(unsigned int pos = 0; pos < seqLen; pos++){</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> simd_int template01 = simdi_load((simd_int *)&dbSeq[pos*VECSIZE_INT*4]);</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> #ifdef AVX2</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="p">@@ -85,7 +81,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> // __m256i score_vec_8bit = _mm256_shuffle_epi8(score_matrix_vec01, template01);</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> // __m256i lookup_mask01 = _mm256_cmpgt_epi8(sixten, template01); // 16 > t</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> // score_vec_8bit = _mm256_and_si256(score_vec_8bit, lookup_mask01);</span>
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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;">-#elif defined(SSE)</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> // each position has 32 byte</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> // 20 scores and 12 zeros</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> // load score 0 - 15</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -96,16 +92,8 @@</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> // _mm_shuffle_epi8</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> // for i ... 16</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> // score01[i] = score_matrix_vec01[template01[i]%16]</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __m128i score01 =vreinterpretq_m128i_u8(vqtbl1q_u8(vreinterpretq_u8_m128i(score_matrix_vec01),vreinterpretq_u8_m128i(template01)));</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> __m128i score01 =_mm_shuffle_epi8(score_matrix_vec01,template01);</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __m128i score16 =vreinterpretq_m128i_u8(vqtbl1q_u8(vreinterpretq_u8_m128i(score_matrix_vec16),vreinterpretq_u8_m128i(template01)));</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> __m128i score16 =_mm_shuffle_epi8(score_matrix_vec16,template01);</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> // t[i] < 16 => 0 - 15</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> // example: template01: 02 15 12 18 < 16 16 16 16 => FF FF FF 00</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> __m128i lookup_mask01 = _mm_cmplt_epi8(template01, sixten);</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="p">@@ -292,7 +280,7 @@</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> EXTRACT_AVX(24); EXTRACT_AVX(25); EXTRACT_AVX(26); EXTRACT_AVX(27);</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> EXTRACT_AVX(28); EXTRACT_AVX(29); EXTRACT_AVX(30); EXTRACT_AVX(31);</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> #undef EXTRACT_AVX</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#elif defined(SSE)</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> #define EXTRACT_SSE(i) score_arr[i] = _mm_extract_epi8(score, i)</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> EXTRACT_SSE(0); EXTRACT_SSE(1); EXTRACT_SSE(2); EXTRACT_SSE(3);</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> EXTRACT_SSE(4); EXTRACT_SSE(5); EXTRACT_SSE(6); EXTRACT_SSE(7);</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/Application.cpp</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/Application.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="p">@@ -4,10 +4,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> #include "DistanceCalculator.h"</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> #include "Timer.h"</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> </span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifndef NEON</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <CpuInfo.h></span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> #include <iomanip></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> extern const char *binary_name;</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="p">@@ -24,30 +20,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> extern std::vector<Categories> categories;</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> void checkCpu() {</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifndef NEON</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CpuInfo info;</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (info.HW_x64 == false) {</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::ERROR) << "64-bit system is required to run MMseqs2.\n";</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXIT(EXIT_FAILURE);</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef SEE</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if(info.HW_SSE41 == false) {</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::ERROR) << "SSE4.1 is required to run MMseqs2.\n";</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXIT(EXIT_FAILURE);</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef AVX2</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (info.HW_AVX2 == false) {</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::ERROR) << "Your machine does not support AVX2.\n";</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (info.HW_SSE41 == true) {</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::ERROR) << "Please recompile with SSE4.1: cmake -DHAVE_SSE4_1=1 \n";</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } else {</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Debug(Debug::ERROR) << "SSE4.1 is the minimum requirement to run MMseqs2.\n";</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXIT(EXIT_FAILURE);</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> Command *getCommandByName(const char *s) {</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/Util.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/Util.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="p">@@ -155,11 +155,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> size_t count, size_t worldRank, size_t worldSize,</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> size_t *start, size_t *size);</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifdef __LP64__</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> template</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> void Util::decomposeDomainByAminoAcid<size_t*>(size_t aaSize, size_t *seqSizes,</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> size_t count, size_t worldRank, size_t worldSize,</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> size_t *start, size_t *size);</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> </span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> </span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> // http://jgamble.ripco.net/cgi-bin/nw.cgi?inputs=8&algorithm=batcher&output=svg</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/lib/ksw2/ksw2_extz2_sse.cpp</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/lib/ksw2/ksw2_extz2_sse.cpp</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="p">@@ -31,24 +31,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> #include <assert.h></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> #include "ksw2.h"</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> </span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "sse2neon.h"</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#define __SSE2__</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#define KSW_SSE2_ONLY</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifndef NEON</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_SSE2_ONLY</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#undef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse4.1.h></span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> #ifdef KSW_CPU_DISPATCH</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> #ifdef __SSE4_1__</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="p">@@ -165,11 +149,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> mask = _mm_or_si128(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> tmp = _mm_cmpeq_epi8(sq, st);</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = _mm_or_si128(_mm_andnot_si128(tmp, sc_mis_), _mm_and_si128(tmp, sc_mch_));</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> tmp = _mm_andnot_si128(mask, tmp);</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> _mm_storeu_si128((__m128i*)((uint8_t*)s + t), tmp);</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="p">@@ -186,22 +166,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> for (t = st_; t <= en_; ++t) {</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> __m128i z, a, b, xt1, vt1, ut, tmp;</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> __dp_code_block1;</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8()</span></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> __dp_code_block2;</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> _mm_store_si128(&x[t], _mm_max_epi8(a, zero_));</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> _mm_store_si128(&y[t], _mm_max_epi8(b, zero_));</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = _mm_cmpgt_epi8(a, zero_);</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _mm_store_si128(&x[t], _mm_and_si128(a, tmp));</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = _mm_cmpgt_epi8(b, zero_);</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _mm_store_si128(&y[t], _mm_and_si128(b, tmp));</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> __m128i *pr = p + r * n_col_ - st_;</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="p">@@ -210,16 +178,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> __dp_code_block1;</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> d = _mm_and_si128(_mm_cmpgt_epi8(a, z), flag1_); // d = a > z? 1 : 0</span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> tmp = _mm_cmpgt_epi8(b, z);</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> d = _mm_blendv_epi8(d, flag2_, tmp); // d = b > z? 2 : d</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = _mm_cmpgt_epi8(b, z);</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, flag2_)); // d = b > z? 2 : d; emulating blendv</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> __dp_code_block2;</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> tmp = _mm_cmpgt_epi8(a, zero_);</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> _mm_store_si128(&x[t], _mm_and_si128(tmp, a));</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="p">@@ -236,16 +197,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> __dp_code_block1;</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), flag1_); // d = z > a? 0 : 1</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> tmp = _mm_cmpgt_epi8(z, b);</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> d = _mm_blendv_epi8(flag2_, d, tmp); // d = z > b? d : 2</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // we need to emulate SSE4.1 intrinsics _mm_max_epi8() and _mm_blendv_epi8()</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = _mm_cmpgt_epi8(z, b);</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- d = _mm_or_si128(_mm_andnot_si128(tmp, flag2_), _mm_and_si128(tmp, d)); // d = z > b? d : 2; emulating blendv</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> __dp_code_block2;</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> tmp = _mm_cmpgt_epi8(zero_, a);</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> _mm_store_si128(&x[t], _mm_andnot_si128(tmp, a));</span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="p">@@ -276,13 +230,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> _mm_storeu_si128((__m128i*)&H[t], H1);</span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> t_ = _mm_set1_epi32(t);</span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> tmp = _mm_cmpgt_epi32(H1, max_H_);</span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);</span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);</span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_H_ = _mm_or_si128(_mm_and_si128(tmp, H1), _mm_andnot_si128(tmp, max_H_));</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- max_t_ = _mm_or_si128(_mm_and_si128(tmp, t_), _mm_andnot_si128(tmp, max_t_));</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> _mm_storeu_si128((__m128i*)HH, max_H_);</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> _mm_storeu_si128((__m128i*)tt, max_t_);</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="p">@@ -334,4 +283,3 @@</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> kfree(km, mem2); kfree(km, off);</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,12 +6,79 @@ export LC_ALL=C.UTF-8</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">export DEB_CXXFLAGS_MAINT_APPEND+=-DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">binprefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr/bin</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">libexecdir=$(prefix)/lib/$(DEB_SOURCE)</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">%:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} ; \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 ; do \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} ; \</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> done</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS)" && export CFLAGS="$(CFLAGS)" && \</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">else</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> dh_auto_configure</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">endif</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">override_dh_auto_build:</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> mkdir -p $(binprefix)</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> dh_auto_build --builddirectory build_$${SIMD} ; \</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> done</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> mkdir -p $(binprefix)</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 ; do \</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> dh_auto_build --builddirectory build_$${SIMD} ; \</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> done</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> dh_auto_build --builddirectory build_plain</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">else</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> dh_auto_build</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">endif</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">override_dh_auto_install:</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
</pre>
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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="plaintext"> dh_auto_install --builddirectory build_$${SIMD} ; \</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> done</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> dh_install usr/bin/mmseqs-* usr/bin/</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> cd $(binprefix) \</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> && for prog in mmseqs ; do \</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 ; do \</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> dh_auto_install --builddirectory build_$${SIMD} ; \</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> done</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> dh_auto_install --builddirectory build_plain</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> dh_install usr/bin/mmseqs-* usr/bin/</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> cd $(binprefix) \</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> && for prog in mmseqs ; do \</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">else</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> dh_auto_install</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> dh_install usr/bin/mmseqs usr/bin/</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">endif</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">override_dh_auto_clean:</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> dh_auto_clean</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" 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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> rm -Rf build-*</span>
</pre>
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81
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15
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">override_dh_install:</span>
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16
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> dh_install</span>
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17
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"> mkdir -p debian/mmseqs2/usr/lib/mmseqs2/test</span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -27,3 +94,6 @@ override_dh_install:</td>
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27
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/*.lib \</span>
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28
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/CovSeqidQscPercMinDiag.out \</span>
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29
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/CovSeqidQscPercMinDiagTargetCov.out || true</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">override_dh_gencontrol:</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> dh_gencontrol -- -Vsimde:Built-Using="$(shell dpkg-query -f '$${source:Package} (= $${source:Version}), ' -W "libsimde-dev")"</span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/de455148ce4ee38e28f6d976b6f246985666bf86...b0a840aa7e4f91a1afe37909d19fe23956d5449c#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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">@@ -7,7 +7,10 @@ Reference:</td>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> Number: 1</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> DOI: 10.1038/s41467-018-04964-5</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> URL: "https://www.nature.com/articles/s41467-018-04964-5"</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Other-References: "https://github.com/soedinglab/MMseqs2"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Repository: https://github.com/soedinglab/MMseqs2.git</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Repository-Browse: https://github.com/soedinglab/MMseqs2</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Bug-Database: https://github.com/soedinglab/MMseqs2/issues</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Bug-Submit: https://github.com/soedinglab/MMseqs2/issues/new</span>
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11
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Registry:</span>
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12
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> - Name: OMICtools</span>
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13
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> Entry: OMICS_11001</span>
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