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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/wtdbg2">Debian Med / wtdbg2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/880ad9aedd8495dc7c0c90280602df885b0ee0fd">880ad9ae</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-18T19:52:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build on all architectures and don't violate the i386/amd64 baselines
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/e4e438f1958c34fcc66d684e9afa63666f9f3086">e4e438f1</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-18T19:52:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install the scripts to /usr/share/wtdbg2/ and add their dependencies under "Suggests"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/wtdbg2/-/commit/8c33edeb9398acfa56d283f86167804de4f9366b">8c33edeb</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-18T19:52:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install the README.md
</pre>
</li>
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<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1a0453e516e167132f0f9392c87de0ea5fe79145">
<span class="new-file">
+
debian/bin/simd-dispatch
</span>
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<span class="new-file">
+
debian/docs
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<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
<span class="new-file">
+
debian/install
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<li class="file-stats">
<a href="#4d4a394ff4174f20019a8af4d8b6185efe92c21f">
debian/patches/hardening.patch
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<li class="file-stats">
<a href="#2f15517af5ccbb849f6d169d0dec02d4b05d0f7d">
<span class="new-file">
+
debian/patches/scripts-tweak
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
<span class="new-file">
+
debian/patches/simde
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</ul>
<h4>Changes:</h4>
<li id="1a0453e516e167132f0f9392c87de0ea5fe79145">
<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#1a0453e516e167132f0f9392c87de0ea5fe79145"><strong>debian/bin/simd-dispatch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PKG</span><span class="o" style="font-weight: 600;">=</span>wtdbg2</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">DIR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASH_SOURCE</span><span class="p">[0]</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1 <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">BASE</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">realpath</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">DIR</span><span class="k" style="font-weight: 600;">}</span>/../lib/<span class="nv" style="color: #008080;">$PKG</span>/<span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">function </span>test_and_run <span class="o" style="font-weight: 600;">()</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> /proc/cpuinfo <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-x</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">BASE</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># echo "${cmd}" "$@"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">cmd</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>SIMD <span class="k" style="font-weight: 600;">in </span>avx2 avx sse4.1 ssse3 sse3 sse2 sse mmx <span class="p">;</span> <span class="k" style="font-weight: 600;">do </span>test_and_run <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SIMD</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fallback to plain option</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nv" style="color: #008080;">$BASE</span><span class="nt" style="color: #000080;">-plain</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">wtdbg2 (2.5-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Build on all architectures and don't violate the i386/amd64 baselines</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #958091</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Install the scripts to /usr/share/wtdbg2/ and add their dependencies under</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> "Suggests"</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Install the README.md</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> Sat, 18 Apr 2020 18:45:55 +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">wtdbg2 (2.5-1) 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"> * Initial release (Closes: #955548)</span>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,8 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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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>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> zlib1g-dev,</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> libsimde-dev</span>
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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/wtdbg2</span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/wtdbg2.git</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">@@ -15,6 +16,10 @@ Package: wtdbg2</td>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${misc:Depends}</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Suggests: ${perl:Depends},</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> minimap2,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> samtools,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> mummer</span>
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18
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Description: de novo sequence assembler for long noisy reads</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Wtdbg2 is a de novo sequence assembler for long noisy reads produced by</span>
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20
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads</span>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">README.md</span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">scripts/* /usr/share/wtdbg2/</span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#4d4a394ff4174f20019a8af4d8b6185efe92c21f"><strong>debian/patches/hardening.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,9 +2,9 @@ Author: Andreas Tille <tille@debian.org></td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Thu, 02 Apr 2020 11:37:59 +0200</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Propagate hardening options</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">a</span>/Makefile</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">b</span>/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -11,12 +11,12 @@</span><span class="idiff left right"> TIMESTAMP=$(shell date)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- <span class="idiff left right">wtdbg2.orig</span>/Makefile</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ <span class="idiff left right">wtdbg2</span>/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -11,12 +11,12 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> ifeq (1, ${DEBUG})</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" 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">@@ -20,3 +20,32 @@ Description: Propagate hardening options</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> GENERIC_SRC=mem_share.h chararray.h sort.h list.h pgzf.h sort.h list.h dna.h thread.h filereader.h filewriter.h bitvec.h bit2vec.h bitsvec.h hashset.h</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> PROGS=kbm2 wtdbg2 wtdbg-cns wtpoa-cns pgzf</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -24,22 +24,22 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> all: $(PROGS)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> kbm2: $(GENERIC_SRC) kbm.c kbm.h kbmpoa.h wtpoa.h tripoa.h poacns.h kswx.h ksw.h ksw.c</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -o $@ kbm.c ksw.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ kbm.c ksw.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> wtdbg2: $(GENERIC_SRC) wtdbg.c wtdbg-graph.h wtdbg.h kbm.h kswx.h ksw.h ksw.c kbmpoa.h wtpoa.h tripoa.h poacns.h</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;">- $(CC) $(CFLAGS) -o $@ wtdbg.c ksw.c $(GLIBS)</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;">+ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ wtdbg.c ksw.c $(GLIBS)</span></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"> wtdbg-cns: $(GENERIC_SRC) wtdbg-cns.c kswx.h ksw.h ksw.c dbgcns.h dagcns.h queue.h general_graph.h</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;">- $(CC) $(CFLAGS) -o wtdbg-cns wtdbg-cns.c ksw.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o wtdbg-cns wtdbg-cns.c ksw.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> wtpoa-cns: $(GENERIC_SRC) wtpoa.h wtpoa-cns.c poacns.h tripoa.h ksw.h ksw.c</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -o $@ wtpoa-cns.c ksw.c $(GLIBS)</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;">+ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ wtpoa-cns.c ksw.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> pgzf: mem_share.h sort.h list.h thread.h pgzf.h pgzf.c</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -o $@ pgzf.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ pgzf.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> best_sam_hits4longreads: $(GENERIC_SRC) best_sam_hits4longreads.c</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(CFLAGS) -o $@ best_sam_hits4longreads.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ best_sam_hits4longreads.c $(GLIBS)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> rm -f *.o *.gcda *.gcno *.gcov gmon.out $(PROGS)</span></pre>
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<li id="2f15517af5ccbb849f6d169d0dec02d4b05d0f7d">
<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#2f15517af5ccbb849f6d169d0dec02d4b05d0f7d"><strong>debian/patches/scripts-tweak</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Use the executables from the Debian 'mummer' package</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- wtdbg2.orig/scripts/mum_assess.sh</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ wtdbg2/scripts/mum_assess.sh</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -5,7 +5,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> REF=$1</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> CTG=$2</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> # change this path to your mummer</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-MUM=/public/software/mummer-323-intel</span></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;">+MUM=/usr/bin</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> if [ -z $REF ] || [ -z $CTG ]; then</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> echo "Usage: $0 <ref> <ctg>"</span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix_install.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">hardening.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">simde</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">scripts-tweak</span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: enable non-X86 building via SIMDe</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- wtdbg2.orig/ksw.c</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ wtdbg2/ksw.c</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -25,7 +25,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #include <stdlib.h></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include <stdint.h></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></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;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/sse2.h"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> #include "ksw.h"</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> #ifdef USE_MALLOC_WRAPPERS</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- wtdbg2.orig/poacns.h</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ wtdbg2/poacns.h</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -25,8 +25,8 @@</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> #include "chararray.h"</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #include "list.h"</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #include "hashset.h"</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <emmintrin.h></span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <tmmintrin.h></span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "simde/x86/ssse3.h"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> #if __BYTE_ORDER == 1234</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> //#pragma message(" ** " __FILE__ " has been tested in LITTLE_ENDIAN **\n")</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- wtdbg2.orig/Makefile</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ wtdbg2/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -11,31 +11,32 @@</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> endif</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"> ifeq (1, ${DEBUG})</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS+=-g3 -W -Wall -Wno-unused-but-set-variable -O0 -DDEBUG=1 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -msse4.2</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+=-g3 -W -Wall -Wno-unused-but-set-variable -O0 -DDEBUG=1 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> else</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS+=-g3 -W -Wall -Wno-unused-but-set-variable -O4 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -msse4.2</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+=-g3 -W -Wall -Wno-unused-but-set-variable -O4 -DVERSION="$(VERSION)" -DRELEASE="$(RELEASE)" -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> endif</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> GLIBS=-lm -lrt -lpthread -lz $(LDFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> GENERIC_SRC=mem_share.h chararray.h sort.h list.h pgzf.h sort.h list.h dna.h thread.h filereader.h filewriter.h bitvec.h bit2vec.h bitsvec.h hashset.h</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-PROGS=kbm2 wtdbg2 wtdbg-cns wtpoa-cns pgzf</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+SFX ?=</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+PROGS=kbm2$(SFX) wtdbg2$(SFX) wtdbg-cns$(SFX) wtpoa-cns$(SFX) pgzf$(SFX)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> all: $(PROGS)</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-kbm2: $(GENERIC_SRC) kbm.c kbm.h kbmpoa.h wtpoa.h tripoa.h poacns.h kswx.h ksw.h ksw.c</span></span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+kbm2$(SFX): $(GENERIC_SRC) kbm.c kbm.h kbmpoa.h wtpoa.h tripoa.h poacns.h kswx.h ksw.h ksw.c</span></span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ kbm.c ksw.c $(GLIBS)</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> </span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-wtdbg2: $(GENERIC_SRC) wtdbg.c wtdbg-graph.h wtdbg.h kbm.h kswx.h ksw.h ksw.c kbmpoa.h wtpoa.h tripoa.h poacns.h</span></span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+wtdbg2$(SFX): $(GENERIC_SRC) wtdbg.c wtdbg-graph.h wtdbg.h kbm.h kswx.h ksw.h ksw.c kbmpoa.h wtpoa.h tripoa.h poacns.h</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ wtdbg.c ksw.c $(GLIBS)</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-wtdbg-cns: $(GENERIC_SRC) wtdbg-cns.c kswx.h ksw.h ksw.c dbgcns.h dagcns.h queue.h general_graph.h</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o wtdbg-cns wtdbg-cns.c ksw.c $(GLIBS)</span></span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+wtdbg-cns$(SFX): $(GENERIC_SRC) wtdbg-cns.c kswx.h ksw.h ksw.c dbgcns.h dagcns.h queue.h general_graph.h</span></span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ wtdbg-cns.c ksw.c $(GLIBS)</span></span>
</pre>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-wtpoa-cns: $(GENERIC_SRC) wtpoa.h wtpoa-cns.c poacns.h tripoa.h ksw.h ksw.c</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+wtpoa-cns$(SFX): $(GENERIC_SRC) wtpoa.h wtpoa-cns.c poacns.h tripoa.h ksw.h ksw.c</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ wtpoa-cns.c ksw.c $(GLIBS)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-pgzf: mem_share.h sort.h list.h thread.h pgzf.h pgzf.c</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+pgzf$(SFX): mem_share.h sort.h list.h thread.h pgzf.h pgzf.c</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> $(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) -o $@ pgzf.c $(GLIBS)</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> best_sam_hits4longreads: $(GENERIC_SRC) best_sam_hits4longreads.c</span></pre>
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<a href="https://salsa.debian.org/med-team/wtdbg2/-/compare/817993111236545c50c1f3bfd544c25eadafb0b9...8c33edeb9398acfa56d283f86167804de4f9366b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,9 +7,62 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">export DEB_CFLAGS_MAINT_APPEND=-DSIMDE_ENABLE_OPENMP -fopenmp-simd</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">export CFLAGS=$(shell dpkg-buildflags --get CFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">export CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">export LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">prefix=$(CURDIR)/debian/$(DEB_SOURCE)/usr</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">libexecdir=$(prefix)/lib/$(DEB_SOURCE)</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> mkdir -p $(prefix)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> export CFLAGS="$(CFLAGS) -m$${SIMD}" ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> make clean ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> dh_auto_build -- SFX=-$${SIMD} ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> done</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> mkdir -p $(prefix)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> mkdir -p $(libexecdir)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> for SIMD in ssse3 sse3 sse2 sse mmx; do \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> export CFLAGS="$(CXXFLAGS) -m$${SIMD}" ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> make clean ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> dh_auto_build -- SFX=-$${SIMD} ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> done</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> dh_auto_build -- SFX=-plain</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">else</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="40" 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">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> dh_auto_build</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="41" 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">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">endif</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="42" 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">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<td class="diff-line-num new_line" data-linenumber="43" 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">
43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">override_dh_auto_install:</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="44" 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">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> for SIMD in avx2 avx sse4.1 ssse3 sse3 sse2 ; do \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> export CFLAGS="$(CFLAGS) -m$${SIMD}" ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> dh_auto_build -- SFX=-$${SIMD} BIN=$(libexecdir) install ; \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> done</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="50" 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">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> mkdir -p $(prefix)/bin</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> cd $(prefix)/bin \</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> && for prog in kbm2 pgzf wtdbg-cns wtdbg2 wtpoa-cns ; do \</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">else ifeq (i386,$(DEB_HOST_ARCH))</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> dh_install debian/bin/simd-dispatch /usr/lib/$(DEB_SOURCE)/</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> for SIMD in sse2 sse mmx ; do \</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> export CFLAGS="$(CFLAGS) -m$${SIMD}" ; \</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> dh_auto_build -- SFX=-$${SIMD} BIN=$(libexecdir) install ; \</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> done</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> export CLFAGS="$(CFLAGS)" ; dh_auto_build -- SFX=-plain BIN=$(libexecdir) \</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> install</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> mkdir -p $(prefix)/bin</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> cd $(prefix)/bin \</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> && for prog in kbm2 pgzf wtdbg-cns wtdbg2 wtpoa-cns ; do \</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> ln -s ../lib/$(DEB_SOURCE)/simd-dispatch $${prog} ; done</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">else</span>
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15
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> make BIN=debian/$(DEB_SOURCE)/usr/bin install</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">endif</span></pre>
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