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GitLab

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<h3>

Michael R. Crusoe pushed to branch debian/experimental

at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/c8a4d932ea7a07d931166099a7bf83158dbb694f">c8a4d932</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-02-26T09:13:02+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Require libsimde-dev (>= 0.7.2-5) for i386

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/7edef2042d3f3a5ce05839acc4637aa1dd5b07f8">7edef204</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-02-26T09:50:14+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix for 32bit systems

</pre>

</li>

</ul>

<h4>5 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="#6459745b355c3512e338fc180c54a8ebebd53eff">

debian/patches/fix_signedness

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#2cd28d22eca59c0013ae61ced8c53c057572bb0f">

<span class="deleted-file">

−

debian/patches/simde_tweak

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/5080a9ed148f2f4bd5797fd72f8d707c1d9d0da3...7edef2042d3f3a5ce05839acc4637aa1dd5b07f8#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mmseqs2 (13-45111+ds-2) UNRELEASED; urgency=medium</span>

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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">  * Team upload.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * Require libsimde-dev (>= 0.7.2-5) for i386</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  Fri, 26 Feb 2021 09:10:06 +0100</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">mmseqs2 (13-45111+ds-1) unstable; urgency=medium</span>

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/5080a9ed148f2f4bd5797fd72f8d707c1d9d0da3...7edef2042d3f3a5ce05839acc4637aa1dd5b07f8#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ Build-Depends-Arch: cmake,</td>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">                    libzstd-dev,</span>

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">                    zlib1g-dev,</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">                    libbz2-dev,</span>

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12

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

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">                    libsimde-dev<span class="idiff left right"> (>= 0.7.2-5)</span>,</span>

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13

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Standards-Version: 4.5.1</span>

</pre>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2</span>

</pre>

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<br>

</li>

<li id="6459745b355c3512e338fc180c54a8ebebd53eff">

<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/5080a9ed148f2f4bd5797fd72f8d707c1d9d0da3...7edef2042d3f3a5ce05839acc4637aa1dd5b07f8#6459745b355c3512e338fc180c54a8ebebd53eff"><strong>debian/patches/fix_signedness</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Milot Mirdita <milot@mirdita.de></span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Thu, 25 Feb 2021 23:32:00 +0100</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Subject: Fix some 32-bit issues #418</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Origin: upstream, https://github.com/soedinglab/MMseqs2/commit/d9744e3c28dadd2cc8c03c8c5c8179400d8fb55a</span></span>

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">and https://github.com/soedinglab/MMseqs2/commit/852f04de365a377b0d24b8382b51c281933d8250</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/ByteParser.h</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/ByteParser.h</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,15 +1,17 @@</span></span>

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

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> #define BYTE_PARSER_H</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include "Debug.h"</span></span>

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

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

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "Debug.h"</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>

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

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

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    static size_t parse(const std::string& sizeAndUnit) {</span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    static uint64_t parse(const std::string& sizeAndUnit) {</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff">         // default unit is M</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        size_t unitFactor = TWO_POW_10 * TWO_POW_10;</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        size_t size = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t unitFactor = TWO_POW_10 * TWO_POW_10;</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t size = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff">         size_t strLen = sizeAndUnit.size();</span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff">         char lastChar = sizeAndUnit[strLen - 1];</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -37,16 +39,16 @@</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff">         </span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        // convert to size_t</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if (1 == sscanf(digitsString.c_str(), "%zu", &size)) {</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            size_t sizeBits = highestOneBitPosition(size);</span></span>

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

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        // convert to uint64_t</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if (1 == sscanf(digitsString.c_str(), "%" PRIu64, &size)) {</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            uint64_t sizeBits = highestOneBitPosition(size);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            uint64_t unitFactorBits = highestOneBitPosition(unitFactor);</span></span>

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

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff">             if ((sizeBits + unitFactorBits) > 64) {</span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                // cannot store (size * unitFactor) in a size_t</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                // cannot store (size * unitFactor) in a uint64_t</span></span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff">                 return INVALID_SIZE;</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            size_t numBytes = (size * unitFactor);</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            uint64_t numBytes = (size * unitFactor);</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff">             return numBytes;</span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff">         } else {</span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff">             // conversion failed</span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -54,15 +56,15 @@</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff">     };</span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff">     </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;">-    static std::string format(size_t numBytes, char unit='a', char accuracy='l') {</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;">-        size_t unitT = TWO_POW_10 * TWO_POW_10 * TWO_POW_10 * TWO_POW_10;</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;">-        size_t unitG = TWO_POW_10 * TWO_POW_10 * TWO_POW_10;</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;">-        size_t unitM = TWO_POW_10 * TWO_POW_10;</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        size_t unitK = TWO_POW_10;</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    static std::string format(uint64_t numBytes, char unit='a', char accuracy='l') {</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t unitT = TWO_POW_10 * TWO_POW_10 * TWO_POW_10 * TWO_POW_10;</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t unitG = TWO_POW_10 * TWO_POW_10 * TWO_POW_10;</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t unitM = TWO_POW_10 * TWO_POW_10;</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t unitK = TWO_POW_10;</span></span>

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

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff">         // in default mode (l), 1,433,600 will be rounded to 1M.</span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff">         // in more informative mode (h), 1,433,600 will be formatted to 1400K.</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        size_t valForModCheck = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t valForModCheck = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff">         if (accuracy != 'l') {</span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff">             valForModCheck = numBytes;</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -82,7 +84,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff">             }</span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        size_t unitFactor = 1;</span></span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t unitFactor = 1;</span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff">         if ((unit == 't') || (unit == 'T')) {</span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff">             unitFactor = unitT;</span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff">         } else if ((unit == 'g') || (unit == 'G')) {</span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="p">@@ -99,7 +101,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff">             EXIT(EXIT_FAILURE);</span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff">         }</span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </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;">-        size_t value = (size_t)(numBytes / unitFactor);</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t value = (uint64_t)(numBytes / unitFactor);</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff">         std::string str(SSTR(value));</span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff">         if (value > 0) {</span>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">             str.append(1, unit);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="p">@@ -107,18 +109,18 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff">         return str;</span>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff">     };</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    static const size_t INVALID_SIZE = SIZE_MAX;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    static const uint64_t INVALID_SIZE = UINT32_MAX;</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> private:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    static size_t highestOneBitPosition(size_t number) {</span></span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        size_t bits = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    static uint64_t highestOneBitPosition(uint64_t number) {</span></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        uint64_t bits = 0;</span></span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff">         while (number != 0) {</span>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff">             bits++;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff">             number >>= 1;</span>

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<pre style="margin: 0;">+<span id="LC108" 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="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        }</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff">         return bits;</span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff">     };</span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </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;">-    static const size_t TWO_POW_10 = 1024;</span></span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    static const uint64_t TWO_POW_10 = 1024;</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> };</span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> #endif</span>

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1

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/prefiltering/IndexTable.h</span></span>

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2

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/prefiltering/IndexTable.h</span></span>

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3

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="diff"><span class="p">@@ -402,7 +402,7 @@</span></span>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/5080a9ed148f2f4bd5797fd72f8d707c1d9d0da3...7edef2042d3f3a5ce05839acc4637aa1dd5b07f8#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">simde_tweak</span>

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2

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1

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

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

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_system_gzstream.patch</span>

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<br>

</li>

<li id="2cd28d22eca59c0013ae61ced8c53c057572bb0f">

<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/5080a9ed148f2f4bd5797fd72f8d707c1d9d0da3...7edef2042d3f3a5ce05839acc4637aa1dd5b07f8#2cd28d22eca59c0013ae61ced8c53c057572bb0f"><strong>debian/patches/simde_tweak</strong>

deleted

</a>

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1

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

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Subject: work around SIMDe NATIVE_ALIASES issue on i386</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/commons/Util.cpp</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/commons/Util.cpp</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -597,41 +597,42 @@</span></span>

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> // Compute reverse complement of k-mer in 2-bit-per-nucleotide encoding (A: 00, C: 01, T: 10, G: 11)</span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> uint64_t Util::revComplement(const uint64_t kmer, const int k) {</span>

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff">     // broadcast 64bit to 128 bit</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __m128i x = _mm_cvtsi64_si128(kmer);</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __m128i x_up = _mm_cvtsi64_si128(kmer >> (uint64_t)4); // shift right by 2 nucleotides</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    simde__m128i x = simde_mm_cvtsi64_si128(kmer);</span></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    simde__m128i x_up = simde_mm_cvtsi64_si128(kmer >> (uint64_t)4); // shift right by 2 nucleotides</span></span>

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

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff">     // create lookup (set 16 bytes in 128 bit)</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff">     // a lookup entry at the index of two nucleotides (4 bit) describes the reverse</span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff">     // complement of these two nucleotide in the higher 4 bits (lookup1) or in the lower 4 bits (lookup2)</span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> #define c (signed char)</span>

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<td class="old_line diff-line-num old" data-linenumber="21" 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="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __m128i lookup1 = _mm_set_epi8(c(0x50),c(0x10),c(0xD0),c(0x90),c(0x40),c(0x00),c(0xC0),c(0x80),</span></span>

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<td class="old_line diff-line-num old" data-linenumber="22" 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="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    simde__m128i lookup1 = simde_mm_set_epi8(c(0x50),c(0x10),c(0xD0),c(0x90),c(0x40),c(0x00),c(0xC0),c(0x80),</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff">                                    c(0x70),c(0x30),c(0xF0),c(0xB0),c(0x60),c(0x20),c(0xE0),c(0xA0));</span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __m128i lookup2 = _mm_set_epi8(c(0x05),c(0x01),c(0x0D),c(0x09),c(0x04),c(0x00),c(0x0C),c(0x08),</span></span>

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<td class="old_line diff-line-num old" data-linenumber="25" 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="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    simde__m128i lookup2 = simde_mm_set_epi8(c(0x05),c(0x01),c(0x0D),c(0x09),c(0x04),c(0x00),c(0x0C),c(0x08),</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">                                    c(0x07),c(0x03),c(0x0F),c(0x0B),c(0x06),c(0x02),c(0x0E),c(0x0A));</span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff">     // set upper 8 bytes to 0 and revert order of lower 8 bytes</span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __m128i upper = _mm_set_epi8(c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    simde__m128i upper = simde_mm_set_epi8(c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),c(0xFF),</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff">                                  0,1,2,3,4,5,6,7);</span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    // _mm_set1_epi8: create 128 bit with all bytes set to given value</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    // simde_mm_set1_epi8: create 128 bit with all bytes set to given value</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff">     // here: 0x0F (00001111) and 0xF0 (11110000)</span>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    // _mm_and_si128: bitwise AND</span></span>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __m128i kmer1 = _mm_and_si128(x, _mm_set1_epi8(c(0x0F))); // get lower 4 bits</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    __m128i kmer2 = _mm_and_si128(x_up, _mm_set1_epi8(c(0x0F))); // get higher 4 bits</span></span>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    // simde_mm_and_si128: bitwise AND</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    simde__m128i kmer1 = simde_mm_and_si128(x, simde_mm_set1_epi8(c(0x0F))); // get lower 4 bits</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;">+    simde__m128i kmer2 = simde_mm_and_si128(x_up, simde_mm_set1_epi8(c(0x0F))); // get higher 4 bits</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> #undef c</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="41" 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="LC41" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="42" 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="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    // use _mm_shuffle_epi8 to look up reverse complement</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    kmer1 = _mm_shuffle_epi8(lookup1, kmer1);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="44" 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="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    kmer2 = _mm_shuffle_epi8(lookup2, kmer2);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    // use simde_mm_shuffle_epi8 to look up reverse complement</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    kmer1 = simde_mm_shuffle_epi8(lookup1, kmer1);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="47" 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="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    kmer2 = simde_mm_shuffle_epi8(lookup2, kmer2);</span></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="49" 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="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    // _mm_or_si128: bitwise OR</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    x = _mm_or_si128(kmer1, kmer2);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    // simde_mm_or_si128: bitwise OR</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    x = simde_mm_or_si128(kmer1, kmer2);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff">     // set upper 8 bytes to 0 and revert order of lower 8 bytes</span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    x = _mm_shuffle_epi8(x, upper);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    x = simde_mm_shuffle_epi8(x, upper);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff">     // shift out the unused nucleotide positions (1 <= k <=32 )</span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff">     // broadcast 128 bit to 64 bit</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="60" 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">

60

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return (((uint64_t)_mm_cvtsi128_si64(x)) >> (uint64_t)(64-2*k));</span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return (((uint64_t)simde_mm_cvtsi128_si64(x)) >> (uint64_t)(64-2*k));</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> </span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"> </span></pre>

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