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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/mmseqs2">Debian Med / mmseqs2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/6512ceb94edee912a698a404c82215220abf0f31">6512ceb9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-24T10:54:29+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install binaries only in the mmseqs2 binary package
not also the mmseqs2-examples binary package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/b65c534de0c9d85d2a5b293b03db08fae5732e42">b65c534d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-24T11:03:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Report the Debian package version instead of "GITDIR-NOTFOUND"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/e5ae3d4ccd2b9bb5600f79e90b6e6654dbf26918">e5ae3d4c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-24T16:42:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Small tweak to simde patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/1144f31325390ab1799aa9ce78d11301f00123b9">1144f313</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-24T21:52:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use a newer libsimde-dev that fixes a bug found by this package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mmseqs2/-/commit/c274189adac033cda0e895146c1f92b6996df313">c274189a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-24T22:21:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 11-e1a1c+ds-2 to unstable
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/e3a820ccee85263953c989e2ca31fd1b14c8d06d...c274189adac033cda0e895146c1f92b6996df313#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mmseqs2 (11-e1a1c+ds-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Install binaries only in the mmseqs2 binary package, not also the</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> mmseqs2-examples binary package</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Report the Debian package version instead of "GITDIR-NOTFOUND"</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Small tweak to simde patch</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Use a newer libsimde-dev that fixes a bug found by this package</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 24 Apr 2020 22:21:06 +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">mmseqs2 (11-e1a1c+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/e3a820ccee85263953c989e2ca31fd1b14c8d06d...c274189adac033cda0e895146c1f92b6996df313#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Shayan Doust <hello@shayandoust.me></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12)<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><span class="idiff left right"> </span> cmake,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> libgzstream-dev,</span>
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9
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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>
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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"> <span class="idiff left right">libsimde-dev</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12)</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><span class="idiff left right">Build-Depends-arch:</span> cmake,</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <span class="idiff left right"> </span>libgzstream-dev,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>libzstd-dev,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <span class="idiff left right"> </span>zlib1g-dev,</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <span class="idiff left right"> </span>libbz2-dev,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <span class="idiff left right"> libsimde-dev (>= 0.0.0.git.20200424)</span></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mmseqs2</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mmseqs2.git</span>
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<li id="4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/e3a820ccee85263953c989e2ca31fd1b14c8d06d...c274189adac033cda0e895146c1f92b6996df313#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,6 +55,24 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> #ifdef AVX512</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> #include <zmmintrin.h.h> // AVX512</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="p">@@ -164,7 +161,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> // integer support (usable with AVX2)</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> #ifndef SIMD_INT</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> #define SIMD_INT</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;">-#include <immintrin.h> // AVX</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/avx2.h></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> #define ALIGN_INT AVX2_ALIGN_INT</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> #define VECSIZE_INT AVX2_VECSIZE_INT</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> //function header</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -231,7 +228,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> #endif //AVX2</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> #ifdef AVX</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;">-#include <immintrin.h> // AVX</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;">+#include <simde/x86/avx.h></span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> // double support (usable with AVX1)</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> #ifndef SIMD_DOUBLE</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> #define SIMD_DOUBLE</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"><span class="p">@@ -284,11 +281,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> #endif //AVX_SUPPORT</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" 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">@@ -76,15 +94,56 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="diff"> // float support</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="diff"> #ifndef SIMD_FLOAT</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="p">@@ -395,<span class="idiff left right">7 +389,6</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -395,<span class="idiff left right">40 +389,7</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="diff"> #define simdi32_i2f(x) _mm_cvtepi32_ps(x) // convert integer to s.p. float</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="diff"> #define simdi_i2fcast(x) _mm_castsi128_ps(x)</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="diff"> #endif //SIMD_INT</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif //SSE</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;">-</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-inline uint16_t simd_hmax16(const __m128i buffer) {</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- uint16x4_t tmp;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = vmax_u16(vget_low_u16(vreinterpretq_u16_m128i(buffer)), vget_high_u16(vreinterpretq_u16_m128i(buffer)));</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = vpmax_u16(tmp, tmp);</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = vpmax_u16(tmp, tmp);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return vget_lane_u16(tmp, 0);</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-inline uint8_t simd_hmax8(const __m128i buffer) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- uint8x8_t tmp;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = vmax_u8(vget_low_u8(vreinterpretq_u8_m128i(buffer)), vget_high_u8(vreinterpretq_u8_m128i(buffer)));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = vpmax_u8(tmp, tmp);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmp = vpmax_u8(tmp, tmp);</span></span>
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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">
117
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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 = vpmax_u8(tmp, tmp);</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return vget_lane_u8(tmp, 0);</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#if 0</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-template <typename F></span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-inline F simd_hmax(const F * in, unsigned int n);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-inline uint16_t simd_hmax16(const __m128i buffer) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SIMDVec* tmp = (SIMDVec*)&buffer;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return simd_hmax<uint16_t>((uint16_t*)tmp->m128_u16, 8);</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;">-}</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> #ifdef NEON</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> inline uint16_t simd_hmax16(const __m128i buffer) {</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="p">@@ -488,7 +481,6 @@</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-inline uint8_t simd_hmax8(const __m128i buffer) {</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SIMDVec* tmp = (SIMDVec*)&buffer;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return simd_hmax<uint8_t>((uint8_t*)tmp->m128_u8, 16);</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> inline uint16_t simd_hmax16(const __m128i buffer)</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> {</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> __m128i tmp1 = _mm_subs_epu16(_mm_set1_epi16((short)65535), buffer);</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="p">@@ -443,7 +404,6 @@</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> __m128i tmp3 = _mm_minpos_epu16(tmp2);</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> return (int8_t)(255 -(int8_t) _mm_cvtsi128_si32(tmp3));</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> }</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#endif</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> #ifdef AVX2</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> inline uint16_t simd_hmax16_avx(const __m256i buffer){</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="p">@@ -488,7 +448,6 @@</span></span>
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88
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="diff"> return 0;</span>
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89
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="diff"> }</span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="diff"> #else</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" 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">@@ -92,7 +151,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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92
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="diff"> inline unsigned short extract_epi16(__m128i v, int pos) {</span>
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93
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="diff"> switch(pos){</span>
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94
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="diff"> case 0: return _mm_extract_epi16(v, 0);</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="p">@@ -503,7 +4<span class="idiff left right">95</span>,6 @@</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="p">@@ -503,7 +4<span class="idiff left right">62</span>,6 @@</span></span>
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96
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="diff"> return 0;</span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="diff"> }</span>
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98
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="diff"> #endif</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" 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">@@ -100,7 +159,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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100
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> </span>
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101
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"> </span>
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102
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"> /* horizontal max */</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="p">@@ -608,7 +5<span class="idiff left right">99</span>,6 @@</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="p">@@ -608,7 +5<span class="idiff left right">66</span>,6 @@</span></span>
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104
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="diff"> //</span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="diff"> //</span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="diff"> //TODO fix this</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -108,7 +167,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="diff"> float __attribute__((aligned(16))) res;</span>
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109
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="diff"> __m128 P; // query 128bit SSE2 register holding 4 floats</span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="diff"> __m128 R;// result</span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="p">@@ -637,7 +<span class="idiff left right">627</span>,6 @@</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="p">@@ -637,7 +<span class="idiff left right">594</span>,6 @@</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="diff"> R = _mm_add_ps(R,P);</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="diff"> _mm_store_ss(&res, R);</span>
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114
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="diff"> return res;</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -150,20 +209,19 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="diff"> if (CMAKE_COMPILER_IS_CLANG)</span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mmseqs2.orig/src/prefiltering/UngappedAlignment.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mmseqs2/src/prefiltering/UngappedAlignment.cpp</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="p">@@ -71,12 +71,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"> simd_int vscore = simdi_setzero();</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="p">@@ -72,11 +72,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="diff"> simd_int vMaxScore = simdi_setzero();</span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="diff"> const simd_int vBias = simdi8_set(bias);</span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>#ifndef AVX2</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="idiff left right"> </span>#ifndef AVX2</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 SSE</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="diff"> const simd_int sixten = simdi8_set(16);</span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="diff"> const simd_int fiveten = simdi8_set(15);</span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>#endif</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="idiff left right"> </span>#endif</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"> for(unsigned int pos = 0; pos < seqLen; pos++){</span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="diff"> simd_int template01 = simdi_load((simd_int *)&dbSeq[pos*VECSIZE_INT*4]);</span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="diff"> #ifdef AVX2</span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="p">@@ -85,7 +8<span class="idiff left right">1</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="p">@@ -85,7 +8<span class="idiff left right">3</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="diff"> // __m256i score_vec_8bit = _mm256_shuffle_epi8(score_matrix_vec01, template01);</span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="diff"> // __m256i lookup_mask01 = _mm256_cmpgt_epi8(sixten, template01); // 16 > t</span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="diff"> // score_vec_8bit = _mm256_and_si256(score_vec_8bit, lookup_mask01);</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -172,7 +230,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="diff"> // each position has 32 byte</span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="diff"> // 20 scores and 12 zeros</span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="diff"> // load score 0 - 15</span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="p">@@ -96,16 +9<span class="idiff left right">2</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="p">@@ -96,16 +9<span class="idiff left right">4</span>,8 @@</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="diff"> // _mm_shuffle_epi8</span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="diff"> // for i ... 16</span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="diff"> // score01[i] = score_matrix_vec01[template01[i]%16]</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,7 +247,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="diff"> // t[i] < 16 => 0 - 15</span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="diff"> // example: template01: 02 15 12 18 < 16 16 16 16 => FF FF FF 00</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="diff"> __m128i lookup_mask01 = _mm_cmplt_epi8(template01, sixten);</span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="p">@@ -292,7 +28<span class="idiff left right">0</span>,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="p">@@ -292,7 +28<span class="idiff left right">2</span>,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="diff"> EXTRACT_AVX(24); EXTRACT_AVX(25); EXTRACT_AVX(26); EXTRACT_AVX(27);</span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="diff"> EXTRACT_AVX(28); EXTRACT_AVX(29); EXTRACT_AVX(30); EXTRACT_AVX(31);</span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="diff"> #undef EXTRACT_AVX</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -283,7 +341,12 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="diff"> tmp = _mm_andnot_si128(mask, tmp);</span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="diff"> _mm_storeu_si128((__m128i*)((uint8_t*)s + t), tmp);</span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff"><span class="p">@@ -186,22 +166,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="p">@@ -181,27 +161,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> x1_ = _mm_cvtsi32_si128(x1);</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> v1_ = _mm_cvtsi32_si128(v1);</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> st_ = st / 16, en_ = en / 16;</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert(en_ - st_ + 1 <= n_col_);</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> if (!with_cigar) { // score only</span>
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287
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="diff"> for (t = st_; t <= en_; ++t) {</span>
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="diff"> __m128i z, a, b, xt1, vt1, ut, tmp;</span>
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="diff"> __dp_code_block1;</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -306,7 +369,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="diff"> } else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment</span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="diff"> __m128i *pr = p + r * n_col_ - st_;</span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff"><span class="p">@@ -210,16 +17<span class="idiff left right">8</span>,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="p">@@ -210,16 +17<span class="idiff left right">7</span>,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="diff"> __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="diff"> __dp_code_block1;</span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="diff"> d = _mm_and_si128(_mm_cmpgt_epi8(a, z), flag1_); // d = a > z? 1 : 0</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -323,7 +386,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="diff"> __dp_code_block2;</span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="diff"> tmp = _mm_cmpgt_epi8(a, zero_);</span>
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<pre style="margin: 0;"> <span id="LC388" 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="LC326" class="line" lang="diff"><span class="p">@@ -236,16 +19<span class="idiff left right">7</span>,9 @@</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="p">@@ -236,16 +19<span class="idiff left right">6</span>,9 @@</span></span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="diff"> __m128i d, z, a, b, xt1, vt1, ut, tmp;</span>
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328
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="diff"> __dp_code_block1;</span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="diff"> d = _mm_andnot_si128(_mm_cmpgt_epi8(z, a), flag1_); // d = z > a? 0 : 1</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -340,7 +403,7 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="diff"> __dp_code_block2;</span>
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="diff"> tmp = _mm_cmpgt_epi8(zero_, a);</span>
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405
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<pre style="margin: 0;"> <span id="LC405" 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="LC343" class="line" lang="diff"><span class="p">@@ -276,13 +2<span class="idiff left right">30</span>,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="p">@@ -276,13 +2<span class="idiff left right">29</span>,8 @@</span></span>
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="diff"> _mm_storeu_si128((__m128i*)&H[t], H1);</span>
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="diff"> t_ = _mm_set1_epi32(t);</span>
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346
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="diff"> tmp = _mm_cmpgt_epi32(H1, max_H_);</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -354,8 +417,41 @@ Subject: Enable building on non-x86 and less than SSE4.1</td>
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354
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="diff"> }</span>
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355
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="diff"> _mm_storeu_si128((__m128i*)HH, max_H_);</span>
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356
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="diff"> _mm_storeu_si128((__m128i*)tt, max_t_);</span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff"><span class="p">@@ -334,4 +28<span class="idiff left right">3</span>,3 @@</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="p">@@ -334,4 +28<span class="idiff left right">2</span>,3 @@</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="diff"> kfree(km, mem2); kfree(km, off);</span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC424" 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="LC425" 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="LC426" 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="LC427" class="line" lang="diff"><span class="p">@@ -620,18 +620,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"> #undef c</span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> // use _mm_shuffle_epi8 to look up reverse complement</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- kmer1 = vreinterpretq_m128i_u8(vqtbl1q_u8(vreinterpretq_u8_m128i(lookup1),vreinterpretq_u8_m128i(kmer1)));</span></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;">-#else</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> kmer1 =_mm_shuffle_epi8(lookup1, kmer1);</span>
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<pre style="margin: 0;">+<span id="LC435" 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="LC436" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- kmer2 = vreinterpretq_m128i_u8(vqtbl1q_u8(vreinterpretq_u8_m128i(lookup2),vreinterpretq_u8_m128i(kmer2)));</span></span>
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<pre style="margin: 0;">+<span id="LC440" 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="LC441" class="line" lang="diff"> kmer2 = _mm_shuffle_epi8(lookup2, kmer2);</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"> </span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"> // _mm_or_si128: bitwise OR</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="p">@@ -639,11 +631,7 @@</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"> // set upper 8 bytes to 0 and revert order of lower 8 bytes</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#ifdef NEON</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- x = vreinterpretq_m128i_u8(vqtbl1q_u8(vreinterpretq_u8_m128i(x),vreinterpretq_u8_m128i(upper)));</span></span>
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<pre style="margin: 0;">+<span id="LC452" 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="LC453" class="line" lang="diff"> x = _mm_shuffle_epi8(x, upper);</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;">-#endif</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"> // shift out the unused nucleotide positions (1 <= k <=32 )</span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"> // broadcast 128 bit to 64 bit</span></pre>
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<a href="https://salsa.debian.org/med-team/mmseqs2/-/compare/e3a820ccee85263953c989e2ca31fd1b14c8d06d...c274189adac033cda0e895146c1f92b6996df313#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,24 +17,26 @@ libexecdir=$(prefix)/lib/$(DEB_SOURCE)</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">override_dh_auto_configure<span class="idiff left right">-arch</span>:</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} ; \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} <span class="idiff left right">-DVERSION_OVERRIDE=$(DEB_VERSION) </span>; \</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 ; do \</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS) -m$${SIMD}" && export CFLAGS="$(CFLAGS) -m$${SIMD}" && \</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} ; \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_$${SIMD} -- -DEXE_SUFFIX=-$${SIMD} <span class="idiff left right">-DVERSION_OVERRIDE=$(DEB_VERSION) </span>; \</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> export CXXFLAGS="$(CXXFLAGS)" && export CFLAGS="$(CFLAGS)" && \</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> dh_auto_configure --builddirectory build_plain -- -DEXE_SUFFIX=-plain<span class="idiff left right"> -DVERSION_OVERRIDE=$(DEB_VERSION)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> dh_auto_configure</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> dh_auto_configure<span class="idiff left right"> -- -DVERSION_OVERRIDE=$(DEB_VERSION)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">override_dh_auto_configure-indep:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">override_dh_auto_build-arch:</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> mkdir -p $(binprefix)</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,37 +52,41 @@ else</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">override_dh_auto_build-indep:</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">override_dh_auto_install-arch:</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> dh_install <span class="idiff left right">-pmmseqs2 </span>debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> dh_auto_install --builddirectory build_$${SIMD} ; \</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> dh_install usr/bin/mmseqs-* usr/bin/</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> dh_install <span class="idiff left right">-pmmseqs2 </span>usr/bin/mmseqs-* usr/bin/</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"> cd $(binprefix) \</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> && for prog in mmseqs ; do \</span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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63
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> dh_install <span class="idiff left right">-pmmseqs2 </span>debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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65
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 ; do \</span>
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66
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> dh_auto_install --builddirectory build_$${SIMD} ; \</span>
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67
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> done</span>
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68
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"> dh_auto_install --builddirectory build_plain</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> dh_install usr/bin/mmseqs-* usr/bin/</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> dh_install <span class="idiff left right">-pmmseqs2 </span>usr/bin/mmseqs-* usr/bin/</span>
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70
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> cd $(binprefix) \</span>
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71
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> && for prog in mmseqs ; do \</span>
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72
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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73
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">else</span>
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74
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> dh_auto_install</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> dh_install usr/bin/mmseqs usr/bin/</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> dh_install <span class="idiff left right">-pmmseqs2 </span>usr/bin/mmseqs usr/bin/</span>
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76
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">endif</span>
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77
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">override_dh_auto_install-indep:</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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78
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">override_dh_auto_clean:</span>
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79
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> dh_auto_clean</span>
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80
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"> rm -Rf build-*</span>
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81
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">override_dh_install:</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">override_dh_install<span class="idiff left right">-arch</span>:</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> dh_install<span class="idiff left right"> --arch</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> mkdir -p debian/mmseqs2/usr/lib/mmseqs2/test</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> cp src/test/*.index debian/mmseqs2/usr/lib/mmseqs2/test/</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> cp src/test/dataGap debian/mmseqs2/usr/lib/mmseqs2/test/</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,12 +94,17 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> #cp -r obj-$(DEB_HOST_MULTIARCH)/src/test debian/mmseqs2/usr/lib/mmseqs2/</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> # We also remove unneeded files & folders like CMake</span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"> rm -r debian/mmseqs2/usr/lib/mmseqs2/test/CMakeFiles \</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> rm -r<span class="idiff left right">f</span> debian/mmseqs2/usr/lib/mmseqs2/test/CMakeFiles \</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"> debian/mmseqs2/usr/lib/mmseqs2/test/*.cmake \</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> debian/mmseqs2/usr/lib/mmseqs2/test/Makefile \</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/*.lib \</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> debian/mmseqs2/usr/lib/mmseqs2/test/Makefile</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">override_dh_install-indep:</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> dh_install --indep</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> # We also remove unneeded files & folders like CMake</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> rm -rf debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/*.lib \</span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/CovSeqidQscPercMinDiag.out \</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"> debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/CovSeqidQscPercMinDiagTargetCov.out<span class="idiff left right"> || true</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> debian/mmseqs2-examples/usr/share/doc/mmseqs2/example-data/CovSeqidQscPercMinDiagTargetCov.out</span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext">override_dh_gencontrol:</span>
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<pre style="margin: 0;"> <span id="LC110" 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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