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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/rapmap/-/commit/f6be793f5bbef20fabd1b046ad0c520840344334">f6be793f</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-06-05T11:09:20+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add non-x86 compatability with libsimde-dev

</pre>

</li>

</ul>

<h4>6 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#0a8d7c289bbb6d9bb3feec5aa0f3e4068bbee285">

debian/patches/portable_pause

</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>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/rapmap/-/commit/f6be793f5bbef20fabd1b046ad0c520840344334#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">rapmap (0.15.0+dfsg-2) UNRELEASED; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Add non-x86 compatability with libsimde-dev</span>

</pre>

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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="plaintext"></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  Fri, 05 Jun 2020 09:40:30 +0200</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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1

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">rapmap (0.15.0+dfsg-1) unstable; urgency=medium</span>

</pre>

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2

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/rapmap/-/commit/f6be793f5bbef20fabd1b046ad0c520840344334#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,7 @@ Build-Depends: debhelper-compat (= 12),</td>

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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">               libcereal-dev,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" 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">

12

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<td class="diff-line-num new_line" data-linenumber="12" 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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">               libjellyfish-2.0-dev,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">               libjemalloc-dev,</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">               libsimde-dev,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">               libsparsehash-dev,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">               libspdlog-dev,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">               libtclap-dev,</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -26,6 +27,7 @@ Package: rapmap</td>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Architecture: amd64</span>

</pre>

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27

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>

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28

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">         ${misc:Depends}</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Built-Using: ${simde:Built-Using}</span>

</pre>

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29

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Description: rapid sensitive and accurate DNA read mapping via quasi-mapping</span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> RapMap is a testing ground for ideas in quasi-mapping / (lightweight /</span>

</pre>

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31

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33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> pseudo) transcriptome alignment. That means that, at this point, it is</span>

</pre>

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<br>

</li>

<li id="0a8d7c289bbb6d9bb3feec5aa0f3e4068bbee285">

<a href="https://salsa.debian.org/med-team/rapmap/-/commit/f6be793f5bbef20fabd1b046ad0c520840344334#0a8d7c289bbb6d9bb3feec5aa0f3e4068bbee285"><strong>debian/patches/portable_pause</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>

</pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>

</pre>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: Add portable pauses</span></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/include/FastxParserThreadUtils.hpp</span></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/include/FastxParserThreadUtils.hpp</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -18,7 +18,13 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/COMBINE-lab/RapMap/pull/49</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/include/FastxParserThreadUtils.hpp</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/include/FastxParserThreadUtils.hpp</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -6,6 +6,9 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #include <chrono></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include <random></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #include <pthread.h></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(__SSE2__)</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="gi" style="color: #000; background-color: #dfd;">+#include <xmmintrin.h> // _mm_pause</span></span>

</pre>

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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">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<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="diff"> // Most of this code is taken directly from https://github.com/geidav/spinlocks-bench/blob/master/os.hpp.</span>

</pre>

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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="diff"> // However, things may be renamed, modified, or randomly mangled over time.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="diff"><span class="p">@@ -18,7 +21,23 @@</span> namespace fastx_parser {</span>

</pre>

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6

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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="diff">     static const size_t MAX_BACKOFF_ITERS = 1024;</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="18" 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="LC18" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff">     ALWAYS_INLINE static void cpuRelax() {</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(__aarch64__) || defined(arm64)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      asm volatile("yield" ::: "memory");</span></span>

</pre>

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11

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__PPC64__) || defined(PPC64) || defined(__ppc64__)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      asm("ori 0,0,0");</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff">       asm("pause");</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      asm("pause");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #if defined(__SSE2__)  // AMD and Intel</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      _mm_pause();</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #elif defined(__i386__) || defined(__x86_64__)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      asm volatile("pause");</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #elif defined(__aarch64__)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      asm volatile("wfe");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

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

27

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

<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #elif defined(__armel__) || defined(__ARMEL__)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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

<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      asm volatile ("nop" ::: "memory");</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #elif defined(__arm__) || defined(__aarch64__)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

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

30

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

<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      __asm__ __volatile__ ("yield" ::: "memory");</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

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

31

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

<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #elif defined(__ia64__)  // IA64</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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

<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      __asm__ __volatile__ ("hint @pause");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

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

33

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

<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #elif defined(__powerpc__) || defined(__ppc__) || defined(__PPC__)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="34" 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">

34

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

<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+       __asm__ __volatile__ ("or 27,27,27" ::: "memory");</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" 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">

35

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

<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #else  // everything else.</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+       asm volatile ("nop" ::: "memory");</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="16" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" 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">

37

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

<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    #endif</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

</td>

<td class="diff-line-num new_line" data-linenumber="38" 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">

38

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff">     }</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

17

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<td class="diff-line-num new_line" data-linenumber="39" 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">

39

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line" data-linenumber="40" 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">

40

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff">     ALWAYS_INLINE void yieldSleep() {</span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/rapmap/-/commit/f6be793f5bbef20fabd1b046ad0c520840344334#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="4" 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">@@ -4,3 +4,4 @@ avoid_privacy_breach.patch</td>

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<td class="diff-line-num old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line" data-linenumber="4" 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">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">spelling</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">portable_pause</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="6" 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">

6

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<td class="diff-line-num new_line" data-linenumber="6" 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">

6

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">no_gomp_needed</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">simde</span></pre>

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<br>

</li>

<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">

<a href="https://salsa.debian.org/med-team/rapmap/-/commit/f6be793f5bbef20fabd1b046ad0c520840344334#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Add non-x86 portability using SIMD Everywhere</span></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/metro/metrohash128crc.cpp</span></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/metro/metrohash128crc.cpp</span></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -24,7 +24,8 @@</span></span>

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6

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

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>

</pre>

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8

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

</pre>

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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;">-#include <nmmintrin.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/sse4.2.h"</span></span>

</pre>

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12

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

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

</pre>

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

</pre>

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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="diff"> #include "metro/platform.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/ksw2pp/ksw2_extd2_sse.c</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/ksw2pp/ksw2_extd2_sse.c</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -3,29 +3,19 @@</span></span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #include <assert.h></span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #include "ksw2pp/ksw2.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" 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="LC24" 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="LC25" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_SSE2_ONLY</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#undef __SSE4_1__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" 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="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> #ifdef __SSE4_1__</span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> void ksw_extd2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">                             int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__SSE2__)</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> void ksw_extd2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff">                             int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</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;">-#endif</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> #else</span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> void ksw_extd2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff">                             int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // ~KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

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

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> #define __dp_code_block1 \</span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff">  z = _mm_load_si128(&s[t]); \</span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -161,13 +151,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">                          st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>

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<pre style="margin: 0;">+<span id="LC53" 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="LC54" class="line" lang="diff">                          tmp = _mm_cmpeq_epi8(sq, st);</span>

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<pre style="margin: 0;">+<span id="LC55" 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="LC56" class="line" lang="diff">                          tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff">                          tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

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<pre style="margin: 0;">+<span id="LC59" 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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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));</span></span>

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<pre style="margin: 0;">+<span id="LC61" 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="LC62" class="line" lang="diff">                          _mm_storeu_si128((__m128i*)((int8_t*)s + t), tmp);</span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff">                  }</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff">          } else {</span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -184,7 +169,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff">                  for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff">                          __m128i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff">                          __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC69" 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="LC70" class="line" lang="diff">                          z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff">                          z = _mm_max_epi8(z, b);</span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff">                          z = _mm_max_epi8(z, a2);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -195,27 +179,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff">                          _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_max_epi8(b,  zero_), qe_));</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">                          _mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, zero_), qe2_));</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">                          _mm_store_si128(&y2[t], _mm_sub_epi8(_mm_max_epi8(b2, zero_), qe2_));</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(a,  z);</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b,  z);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(a2, z);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" 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="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b2, z);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b2));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmplt_epi8(sc_mch_, z);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         __dp_code_block2;</span></span>

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<pre style="margin: 0;">+<span id="LC89" 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="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b, zero_);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_and_si128(tmp, b),  qe_));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(a2, zero_);</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" 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="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&x2[t], _mm_sub_epi8(_mm_and_si128(tmp, a2), qe2_));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         tmp = _mm_cmpgt_epi8(b2, zero_);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                         _mm_store_si128(&y2[t], _mm_sub_epi8(_mm_and_si128(tmp, b2), qe2_));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" 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="LC98" class="line" lang="diff">                  }</span>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff">          } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff">                         __m128i *pr = p + (size_t)r * n_col_ - st_;</span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -223,7 +186,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff">                                 __m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC105" 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="LC106" class="line" lang="diff">                                 d = _mm_and_si128(_mm_cmpgt_epi8(a, z), _mm_set1_epi8(1));       // d = a  > z? 1 : 0</span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(2), _mm_cmpgt_epi8(b,  z)); // d = b  > z? 2 : d</span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="p">@@ -233,22 +195,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(4), _mm_cmpgt_epi8(b2, z)); // d = a2 > z? 3 : d</span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff">                                 z = _mm_max_epi8(z, b2);</span>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff">                                 z = _mm_min_epi8(z, sc_mch_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a,  z);</span></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;">-                                d = _mm_and_si128(tmp, _mm_set1_epi8(1));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b,  z);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" 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, _mm_set1_epi8(2)));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</span></span>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a2, z);</span></span>

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<pre style="margin: 0;">+<span id="LC121" 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, _mm_set1_epi8(3)));</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2));</span></span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b2, z);</span></span>

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<pre style="margin: 0;">+<span id="LC124" 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, _mm_set1_epi8(4)));</span></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;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b2));</span></span>

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmplt_epi8(sc_mch_, z);</span></span>

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));</span></span>

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<pre style="margin: 0;">+<span id="LC128" 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="LC129" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a, zero_);</span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="p">@@ -270,7 +216,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff">                                 __m128i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC136" 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="LC137" class="line" lang="diff">                                 d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), _mm_set1_epi8(1));    // d = z > a?  0 : 1</span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(2), d, _mm_cmpgt_epi8(z, b));  // d = z > b?  d : 2</span>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -280,22 +225,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(4), d, _mm_cmpgt_epi8(z, b2)); // d = z > b2? d : 4</span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff">                                 z = _mm_max_epi8(z, b2);</span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff">                                 z = _mm_min_epi8(z, sc_mch_);</span>

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<pre style="margin: 0;">+<span id="LC144" 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="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a);</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_andnot_si128(tmp, _mm_set1_epi8(1));</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a));</span></span>

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<pre style="margin: 0;">+<span id="LC148" 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="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(2)));</span></span>

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b));</span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a2);</span></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(3)));</span></span>

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a2));</span></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, b2);</span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(4)));</span></span>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b2));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmplt_epi8(sc_mch_, z);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, sc_mch_), _mm_andnot_si128(tmp, z));</span></span>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff">                                 __dp_code_block2;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(zero_, a);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_andnot_si128(tmp, a),  qe_));</span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="p">@@ -330,13 +259,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff">                                         _mm_storeu_si128((__m128i*)&H[t], H1);</span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff">                                         t_ = _mm_set1_epi32(t);</span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff">                                         tmp = _mm_cmpgt_epi32(H1, max_H_);</span>

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<pre style="margin: 0;">+<span id="LC167" 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="LC168" class="line" lang="diff">                                         max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff">                                         max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);</span>

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<pre style="margin: 0;">+<span id="LC170" 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="LC171" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC172" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC173" 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="LC174" class="line" lang="diff">                                 }</span>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)HH, max_H_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)tt, max_t_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="p">@@ -391,4 +315,3 @@</span></span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff">                 kfree(km, mem2); kfree(km, off);</span>

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/ksw2pp/ksw2_extf2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/ksw2pp/ksw2_extf2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="p">@@ -1,22 +1,16 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> #include <string.h></span>

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<td class="diff-line-num new new_line" data-linenumber="186" 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="LC186" class="line" lang="diff"> #include "ksw2pp/ksw2.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC189" 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="LC190" 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="LC191" 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="LC192" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="193" 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="LC193" class="line" lang="diff"> #ifdef __SSE4_1__</span>

</pre>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_CPU_DISPATCH</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> void ksw_extf2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  void ksw_extf2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez)</span></span>

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<pre style="margin: 0;">+<span id="LC202" 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="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__SSE2__)</span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+void ksw_extf2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez)</span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> #else</span>

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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> void ksw_extf2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t mch, int8_t mis, int8_t e, int w, int xdrop, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // ~KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> {</span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff">         int32_t r, t, tlen_, qlen_, last_st, last_en, H0 = 0, last_H0_t = 0;</span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff">         uint8_t *qr, *sf, *mem;</span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="p">@@ -60,11 +54,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff">                         sq = _mm_loadu_si128((__m128i*)&sf[t]);</span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff">                         st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff">                         tmp = _mm_cmpeq_epi8(sq, st);</span>

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<pre style="margin: 0;">+<span id="LC216" 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="LC217" class="line" lang="diff">                         tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</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;">-#else</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;">-                        tmp = _mm_or_si128(_mm_andnot_si128(tmp, sc_mis_), _mm_and_si128(tmp, sc_mch_));</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;">-#endif</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff">                         _mm_storeu_si128((__m128i*)((uint8_t*)s + t), tmp);</span>

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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff">                 }</span>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff">                 for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="p">@@ -75,12 +65,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff">                         vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); // vt1 <- v[r-1][t-1..t+14]</span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff">                         v1_ = tmp;</span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff">                         ut = _mm_load_si128(&u[t]);                      // ut <- u[t..t+15]</span>

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<pre style="margin: 0;">+<span id="LC228" 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="LC229" class="line" lang="diff">                         z = _mm_max_epi8(z, vt1);                        // z = z > a? z : a (signed)</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;">-#else</span></span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        z = _mm_and_si128(z, _mm_cmpgt_epi8(z, _mm_setzero_si128()));  // z = z > 0? z : 0;</span></span>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        z = _mm_max_epu8(z, vt1);                        // z = max(z, a); this works because both are non-negative</span></span>

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<pre style="margin: 0;">+<span id="LC233" 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="LC234" class="line" lang="diff">                         z = _mm_max_epu8(z, ut);                         // z = max(z, b); this works because both are non-negative</span>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff">                         _mm_store_si128(&u[t], _mm_sub_epi8(z, vt1));    // u[r][t..t+15] <- z - v[r-1][t-1..t+14]</span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff">                         _mm_store_si128(&v[t], _mm_sub_epi8(z, ut));     // v[r][t..t+15] <- z - u[r-1][t..t+15]</span>

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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="p">@@ -104,4 +89,3 @@</span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff">         else ez->zdropped = 1;</span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff">         kfree(km, mem);</span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> }</span>

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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 // __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/ksw2pp/ksw2_exts2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/ksw2pp/ksw2_exts2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="p">@@ -3,29 +3,19 @@</span></span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> #include <assert.h></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> #include "ksw2pp/ksw2.h"</span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC249" 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="LC250" 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="LC251" 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="LC252" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_SSE2_ONLY</span></span>

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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#undef __SSE4_1__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC255" 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="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

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<pre style="margin: 0;">+<span id="LC259" 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="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> #ifdef __SSE4_1__</span>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> void ksw_exts2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff">                                    int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">+<span id="LC265" 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="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__SSE2__)</span></span>

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> void ksw_exts2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff">                                    int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)</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;">-#endif</span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> #else</span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> void ksw_exts2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,</span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff">                                    int8_t q, int8_t e, int8_t q2, int8_t noncan, int zdrop, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // ~KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> {</span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> #define __dp_code_block1 \</span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff">         z = _mm_load_si128(&s[t]); \</span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="p">@@ -161,13 +151,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff">                                 st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>

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<pre style="margin: 0;">+<span id="LC280" 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="LC281" class="line" lang="diff">                                 tmp = _mm_cmpeq_epi8(sq, st);</span>

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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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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);</span>

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<pre style="margin: 0;">+<span id="LC285" 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="LC286" 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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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));</span></span>

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<pre style="margin: 0;">+<span id="LC288" 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="LC289" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)((int8_t*)s + t), tmp);</span>

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff">                 } else {</span>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="p">@@ -184,7 +169,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff">                                 __m128i z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC296" 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="LC297" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff">                                 z = _mm_max_epi8(z, b);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff">                                 z = _mm_max_epi8(z, a2a);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="p">@@ -193,23 +177,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff">                                 _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_max_epi8(b,  zero_), qe_));</span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff">                                 tmp = _mm_load_si128(&donor[t]);</span>

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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff">                                 _mm_store_si128(&x2[t], _mm_sub_epi8(_mm_max_epi8(a2, tmp), q2_));</span>

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<pre style="margin: 0;">+<span id="LC304" 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="LC305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a,  z);</span></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;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

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<pre style="margin: 0;">+<span id="LC307" 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="LC308" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</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;">-                                tmp = _mm_cmpgt_epi8(a2a, z);</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_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2a));</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;">-                                __dp_code_block2;</span></span>

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<pre style="margin: 0;">+<span id="LC312" 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="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span></span>

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<pre style="margin: 0;">+<span id="LC314" 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="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                _mm_store_si128(&y[t],  _mm_sub_epi8(_mm_and_si128(tmp, b),  qe_));</span></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;">-                                tmp = _mm_load_si128(&donor[t]); // TODO: check if this is correct</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(a2, tmp);</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;">-                                tmp = _mm_or_si128(_mm_andnot_si128(tmp, tmp), _mm_and_si128(tmp, a2));</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;">-                                _mm_store_si128(&x2[t], _mm_sub_epi8(tmp, q2_));</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;">-#endif</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff">                 } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff">                         __m128i *pr = p + r * n_col_ - st_;</span>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="p">@@ -217,24 +184,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff">                                 __m128i d, z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp, tmp2;</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"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff">                                 d = _mm_and_si128(_mm_cmpgt_epi8(a, z), _mm_set1_epi8(1));       // d = a  > z? 1 : 0</span>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(2), _mm_cmpgt_epi8(b,  z)); // d = b  > z? 2 : d</span>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff">                                 z = _mm_max_epi8(z, b);</span>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff">                                 d = _mm_blendv_epi8(d, _mm_set1_epi8(3), _mm_cmpgt_epi8(a2a, z)); // d = a2 > z? 3 : d</span>

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff">                                 z = _mm_max_epi8(z, a2a);</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;">-#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="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a,  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_and_si128(tmp, _mm_set1_epi8(1));</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;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(b,  z);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC340" 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, _mm_set1_epi8(2)));</span></span>

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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, b));</span></span>

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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(a2a, z);</span></span>

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<pre style="margin: 0;">+<span id="LC343" 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, _mm_set1_epi8(3)));</span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_andnot_si128(tmp, z), _mm_and_si128(tmp, a2a));</span></span>

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<pre style="margin: 0;">+<span id="LC345" 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="LC346" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a, zero_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_and_si128(tmp, a),  qe_));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="p">@@ -245,11 +200,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff">                                 tmp2 = _mm_load_si128(&donor[t]);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a2, tmp2);</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;">-#ifdef __SSE4_1__</span></span>

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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff">                                 tmp2 = _mm_max_epi8(a2, tmp2);</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;">-#else</span></span>

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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp2 = _mm_or_si128(_mm_andnot_si128(tmp, tmp2), _mm_and_si128(tmp, a2));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC357" 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="LC358" class="line" lang="diff">                                 _mm_store_si128(&x2[t], _mm_sub_epi8(tmp2, q2_));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff">                                 d = _mm_or_si128(d, _mm_and_si128(tmp, _mm_set1_epi8(0x20)));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff">                                 _mm_store_si128(&pr[t], d);</span>

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="p">@@ -260,24 +211,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff">                                 __m128i d, z, a, b, a2, a2a, xt1, x2t1, vt1, ut, tmp, tmp2;</span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC365" 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="LC366" class="line" lang="diff">                                 d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), _mm_set1_epi8(1));    // d = z > a?  0 : 1</span>

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff">                                 z = _mm_max_epi8(z, a);</span>

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(2), d, _mm_cmpgt_epi8(z, b));  // d = z > b?  d : 2</span>

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff">                                 z = _mm_max_epi8(z, b);</span>

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff">                                 d = _mm_blendv_epi8(_mm_set1_epi8(3), d, _mm_cmpgt_epi8(z, a2a)); // d = z > a2? d : 3</span>

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff">                                 z = _mm_max_epi8(z, a2a);</span>

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<pre style="margin: 0;">+<span id="LC372" 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="LC373" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a);</span></span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_andnot_si128(tmp, _mm_set1_epi8(1));</span></span>

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a));</span></span>

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<pre style="margin: 0;">+<span id="LC376" 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="LC377" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(2)));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, b));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_cmpgt_epi8(z, a2a);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                d = _mm_or_si128(_mm_and_si128(tmp, d), _mm_andnot_si128(tmp, _mm_set1_epi8(3)));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="381" 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="LC381" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                z = _mm_or_si128(_mm_and_si128(tmp, z), _mm_andnot_si128(tmp, a2a));</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff">                                 __dp_code_block2;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="384" 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="LC384" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(zero_, a);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff">                                 _mm_store_si128(&x[t],  _mm_sub_epi8(_mm_andnot_si128(tmp, a),  qe_));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="p">@@ -288,11 +227,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="388" 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="LC388" class="line" lang="diff">                                 tmp2 = _mm_load_si128(&donor[t]);</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="389" 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="LC389" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(tmp2, a2);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE4_1__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff">                                 tmp2 = _mm_max_epi8(tmp2, a2);</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="392" 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="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp2 = _mm_or_si128(_mm_andnot_si128(tmp, a2), _mm_and_si128(tmp, tmp2));</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="394" 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="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="395" 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="LC395" class="line" lang="diff">                                 _mm_store_si128(&x2[t], _mm_sub_epi8(tmp2, q2_));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff">                                 d = _mm_or_si128(d, _mm_andnot_si128(tmp, _mm_set1_epi8(0x20))); // d = a > 0? 1<<5 : 0</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="397" 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="LC397" class="line" lang="diff">                                 _mm_store_si128(&pr[t], d);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="p">@@ -316,13 +251,8 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff">                                         _mm_storeu_si128((__m128i*)&H[t], H1);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff">                                         t_ = _mm_set1_epi32(t);</span>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff">                                         tmp = _mm_cmpgt_epi32(H1, max_H_);</span>

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<pre style="margin: 0;">+<span id="LC402" 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="LC403" class="line" lang="diff">                                         max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);</span>

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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff">                                         max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);</span>

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<pre style="margin: 0;">+<span id="LC405" 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="LC406" 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="LC407" 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="LC408" 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="LC409" class="line" lang="diff">                                 }</span>

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)HH, max_H_);</span>

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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)tt, max_t_);</span>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="p">@@ -373,4 +303,3 @@</span></span>

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff">                 kfree(km, mem2); kfree(km, off);</span>

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/ksw2pp/ksw2_extz2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/ksw2pp/ksw2_extz2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="p">@@ -2,26 +2,16 @@</span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> #include <assert.h></span>

</pre>

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421

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> #include "ksw2pp/ksw2.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="426" 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="LC426" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_SSE2_ONLY</span></span>

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<pre style="margin: 0;">+<span id="LC427" 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="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC429" 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="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/sse4.1.h"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> #ifdef __SSE4_1__</span>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">+<span id="LC437" 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="LC438" class="line" lang="diff"> void ksw_extz2_sse41(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__SSE2__)</span></span>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> void ksw_extz2_sse2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">+<span id="LC442" 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="LC443" class="line" lang="diff"> #else</span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)</span>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // ~KSW_CPU_DISPATCH</span></span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"> {</span>

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> #define __dp_code_block1 \</span>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff">         z = _mm_add_epi8(_mm_load_si128(&s[t]), qe2_); \</span>

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="p">@@ -129,13 +119,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff">                                 st = _mm_loadu_si128((__m128i*)&qrr[t]);</span>

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<pre style="margin: 0;">+<span id="LC452" 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="LC453" class="line" lang="diff">                                 tmp = _mm_cmpeq_epi8(sq, st);</span>

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<pre style="margin: 0;">+<span id="LC454" 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="LC455" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(sc_mis_, sc_mch_, tmp);</span>

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff">                                 tmp = _mm_blendv_epi8(tmp,     sc_N_,   mask);</span>

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<pre style="margin: 0;">+<span id="LC457" 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="LC458" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                                tmp = _mm_or_si128(_mm_andnot_si128(mask, tmp),     _mm_and_si128(mask, sc_N_));</span></span>

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<pre style="margin: 0;">+<span id="LC460" 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="LC461" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)((uint8_t*)s + t), tmp);</span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff">                 } else {</span>

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="p">@@ -151,22 +136,10 @@</span></span>

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff">                         for (t = st_; t <= en_; ++t) {</span>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff">                                 __m128i z, a, b, xt1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC468" 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="LC469" 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="LC470" 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="LC471" 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="LC472" 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="LC473" 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="LC474" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">+<span id="LC475" 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="LC476" 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="LC477" class="line" lang="diff">                                 _mm_store_si128(&y[t], _mm_max_epi8(b, zero_));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC478" 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="LC479" 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="LC480" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC481" 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="LC482" 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="LC483" 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="LC484" class="line" lang="diff">                         }</span>

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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff">                 } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff">                         __m128i *pr = p + (size_t)r * n_col_ - st_;</span>

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="p">@@ -175,16 +148,9 @@</span></span>

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff">                                 __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC490" 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="LC491" 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="LC492" 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="LC493" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(b, z);</span>

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<pre style="margin: 0;">+<span id="LC494" 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="LC495" 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="LC496" 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="LC497" 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="LC498" 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="LC499" 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="LC500" 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="LC501" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(a, zero_);</span>

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<pre style="margin: 0;">+<span id="LC503" 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="LC504" class="line" lang="diff"><span class="p">@@ -201,16 +167,9 @@</span></span>

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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff">                                 __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>

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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff">                                 __dp_code_block1;</span>

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<pre style="margin: 0;">+<span id="LC507" 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="LC508" 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="LC509" 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="LC510" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(z, b);</span>

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<pre style="margin: 0;">+<span id="LC511" 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="LC512" 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="LC513" 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="LC514" 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="LC515" 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="LC516" 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="LC517" 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="LC518" class="line" lang="diff">                                 __dp_code_block2;</span>

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff">                                 tmp = _mm_cmpgt_epi8(zero_, a);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC520" 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="LC521" class="line" lang="diff"><span class="p">@@ -241,13 +200,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff">                                         _mm_storeu_si128((__m128i*)&H[t], H1);</span>

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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff">                                         t_ = _mm_set1_epi32(t);</span>

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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff">                                         tmp = _mm_cmpgt_epi32(H1, max_H_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC525" 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="LC526" class="line" lang="diff">                                         max_H_ = _mm_blendv_epi8(max_H_, H1, tmp);</span>

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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff">                                         max_t_ = _mm_blendv_epi8(max_t_, t_, tmp);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC528" 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="LC529" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC530" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC531" 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="LC532" class="line" lang="diff">                                 }</span>

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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)HH, max_H_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff">                                 _mm_storeu_si128((__m128i*)tt, max_t_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="p">@@ -302,4 +256,3 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff">                 kfree(km, mem2); kfree(km, off);</span>

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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff">         }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/ksw2pp/ksw2_gg2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/ksw2pp/ksw2_gg2_sse.c</span></span>

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="p">@@ -1,12 +1,8 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> #include <stdio.h> // for debugging only</span>

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> #include "ksw2pp/ksw2.h"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC547" 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="LC548" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC549" 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="LC550" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <smmintrin.h></span></span>

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<pre style="margin: 0;">+<span id="LC551" 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="LC552" 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="LC553" 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="LC554" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> int ksw_gg2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int *m_cigar_, int *n_cigar_, uint32_t **cigar_)</span>

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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> {</span>

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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="p">@@ -86,16 +82,9 @@</span></span>

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff">                         b = _mm_add_epi8(_mm_load_si128(&y[t]), ut); // b <- y[r-1][t..t+15] + u[r-1][t..t+15]</span>

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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff">                         d = _mm_and_si128(_mm_cmpgt_epi8(a, z), flag1_); // d = a > z? 1 : 0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC561" 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="LC562" class="line" lang="diff">                         z = _mm_max_epi8(z, a);                          // z = z > a? z : a (signed)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff">                         tmp = _mm_cmpgt_epi8(b, z);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff">                         d = _mm_blendv_epi8(d, flag2_, tmp);             // d = b > z? 2 : d</span>

</pre>

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<pre style="margin: 0;">+<span id="LC565" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC566" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC567" 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="LC568" 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="LC569" 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>

</pre>

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<pre style="margin: 0;">+<span id="LC570" 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="LC571" class="line" lang="diff">                         z = _mm_max_epu8(z, b);                          // z = max(z, b); this works because both are non-negative</span>

</pre>

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff">                         _mm_store_si128(&u[t], _mm_sub_epi8(z, vt1)); // u[r][t..t+15] <- z - v[r-1][t-1..t+14]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff">                         _mm_store_si128(&v[t], _mm_sub_epi8(z, ut));  // v[r][t..t+15] <- z - u[r-1][t..t+15]</span>

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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="p">@@ -124,4 +113,3 @@</span></span>

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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff">         kfree(km, mem2); kfree(km, off);</span>

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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff">         return H0;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> }</span>

</pre>

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif // __SSE2__</span></span>

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/ksw2pp/KSW2Aligner.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/ksw2pp/KSW2Aligner.cpp</span></span>

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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="p">@@ -27,10 +27,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff">         asm volatile ("cpuid"</span>

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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff">                         : "=a" (cpuid[0]), "=b" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])</span>

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<td class="diff-line-num new new_line" data-linenumber="584" 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="LC584" class="line" lang="diff">                         : "0" (func_id), "2" (subfunc_id));</span>

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else // on 32bit, ebx can NOT be used as PIC code</span></span>

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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__i386__) // on 32bit, ebx can NOT be used as PIC code</span></span>

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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff">         asm volatile ("xchgl %%ebx, %1; cpuid; xchgl %%ebx, %1"</span>

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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff">                         : "=a" (cpuid[0]), "=r" (cpuid[1]), "=c" (cpuid[2]), "=d" (cpuid[3])</span>

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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff">                         : "0" (func_id), "2" (subfunc_id));</span>

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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        cpuid[0] = 0</span></span>

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"> #endif</span>

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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"> #endif</span>

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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- rapmap.orig/src/CMakeLists.txt</span></span>

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ rapmap/src/CMakeLists.txt</span></span>

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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="p">@@ -87,20 +87,36 @@</span></span>

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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> check_ipo_supported(RESULT HAS_IPOHAS_IPO)</span>

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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> add_library(ksw2pp_sse2 OBJECT ${KSW2PP_ADVANCED_LIB_SRCS})</span>

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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_library(ksw2pp_sse4 OBJECT ${KSW2PP_ADVANCED_LIB_SRCS})</span></span>

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<td class="diff-line-num new new_line" data-linenumber="602" 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">

602

</td>

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

<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> add_library(ksw2pp_basic OBJECT ${KSW2PP_BASIC_LIB_SRCS})</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="603" 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">

603

</td>

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

<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set_target_properties(ksw2pp_basic PROPERTIES INCLUDE_DIRECTORIES ${GAT_SOURCE_DIR}/include)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="604" 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">

604

</td>

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

<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="605" 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">

605

</td>

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

<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set_target_properties(ksw2pp_sse2 PROPERTIES COMPILE_FLAGS "-O3 -msse2 -mno-sse4.1")</span></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="606" 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">

606

</td>

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

<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set_target_properties(ksw2pp_sse2 PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;KSW_SSE2_ONLY;HAVE_KALLOC")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="607" 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">

607

</td>

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

<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set_target_properties(ksw2pp_sse4 PROPERTIES COMPILE_FLAGS "-O3 -msse4.1")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="608" 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">

608

</td>

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

<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set_target_properties(ksw2pp_sse4 PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="609" 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">

609

</td>

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

<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set_target_properties(ksw2pp_basic PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="610" 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">

610

</td>

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

<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(NOT DEFINED CMAKE_SYSTEM_PROCESSOR)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="611" 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">

611

</td>

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

<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  EXECUTE_PROCESS( COMMAND uname -m COMMAND tr -d '\n' OUTPUT_VARIABLE ARCHITECTURE )</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="612" 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">

612

</td>

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

<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  set(CMAKE_SYSTEM_PROCESSOR "${ARCHITECTURE}")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="613" 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">

613

</td>

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

<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="614" 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">

614

</td>

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

<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="615" 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">

615

</td>

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

<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set_target_properties(ksw2pp_basic PROPERTIES INCLUDE_DIRECTORIES ${GAT_SOURCE_DIR}/include)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="616" 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">

616

</td>

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

<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set_target_properties(ksw2pp_sse4 PROPERTIES INCLUDE_DIRECTORIES ${GAT_SOURCE_DIR}/include)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="617" 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">

617

</td>

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

<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="618" 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">

618

</td>

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

<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    set(CMAKE_SYSTEM_PROCESSOR "amd64")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="619" 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">

619

</td>

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

<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "i686")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="620" 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">

620

</td>

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

<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    set(CMAKE_SYSTEM_PROCESSOR "i386")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="621" 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">

621

</td>

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

<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="622" 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">

622

</td>

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

<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="623" 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">

623

</td>

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

<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+message("CMAKE_SYSTEM_PROCESSOR: ${CMAKE_SYSTEM_PROCESSOR}")</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="624" 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">

624

</td>

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

<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="625" 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">

625

</td>

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

<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if("${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "amd64" OR "${CMAKE_SYSTEM_PROCESSOR}" STREQUAL "i386")</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="626" 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">

626

</td>

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

<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  add_library(ksw2pp_sse4 OBJECT ${KSW2PP_ADVANCED_LIB_SRCS})</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="627" 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">

627

</td>

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

<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  set_target_properties(ksw2pp_sse2 PROPERTIES COMPILE_FLAGS "-O3 -msse2 -mno-sse4.1")</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="628" 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">

628

</td>

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

<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  set_target_properties(ksw2pp_sse2 PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;KSW_SSE2_ONLY;HAVE_KALLOC")</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="629" 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">

629

</td>

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

<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  set_target_properties(ksw2pp_sse4 PROPERTIES COMPILE_FLAGS "-O3 -msse4.1")</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="630" 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">

630

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

<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  set_target_properties(ksw2pp_sse4 PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="631" 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">

631

</td>

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

<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  set_target_properties(ksw2pp_basic PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="632" 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">

632

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

<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  set_target_properties(ksw2pp_sse4 PROPERTIES INCLUDE_DIRECTORIES ${GAT_SOURCE_DIR}/include)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="633" 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">

633

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

<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  add_library(ksw2pp STATIC $<TARGET_OBJECTS:ksw2pp_sse2> $<TARGET_OBJECTS:ksw2pp_sse4> $<TARGET_OBJECTS:ksw2pp_basic>)</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="634" 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">

634

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

<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+else()</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="635" 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">

635

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

<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  add_library(ksw2pp STATIC $<TARGET_OBJECTS:ksw2pp_sse2> $<TARGET_OBJECTS:ksw2pp_basic>)</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="636" 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">

636

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

<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif()</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="637" 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">

637

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

<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"> </span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="638" 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">

638

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

<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"> # Build the ksw2pp library</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="639" 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">

639

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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-add_library(ksw2pp STATIC $<TARGET_OBJECTS:ksw2pp_sse2> $<TARGET_OBJECTS:ksw2pp_sse4> $<TARGET_OBJECTS:ksw2pp_basic>)</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="640" 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">

640

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

<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"> set_target_properties(ksw2pp PROPERTIES COMPILE_DEFINITIONS "KSW_CPU_DISPATCH;HAVE_KALLOC")</span>

</pre>

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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> if(HAS_IPO)</span>

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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff">   set_property(TARGET ksw2pp PROPERTY INTERPROCEDURAL_OPTIMIZATION True)</span></pre>

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<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/rapmap/-/commit/f6be793f5bbef20fabd1b046ad0c520840344334#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" 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="24" 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">@@ -24,3 +24,6 @@ override_dh_auto_build:</td>

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24

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24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>

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25

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25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">override_dh_clean:</span>

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26

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26

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">     dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam</span>

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27

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

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

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<pre style="margin: 0;">+<span id="LC29" 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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