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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/hisat2">Debian Med / hisat2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hisat2/-/commit/2ad3dc9b705b8ff32228e498883fb97320a249b4">2ad3dc9b</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-06-20T17:43:39+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forward patches upstream
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
debian/patches/hardening
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<li class="file-stats">
<a href="#2b2f955d1de9cb2d63191eb231f921af08889937">
debian/patches/reproducibile
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<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<h4>Changes:</h4>
<li id="d6c09299b1f914372840e8fd6fcc850f8a11b236">
<a href="https://salsa.debian.org/med-team/hisat2/-/commit/2ad3dc9b705b8ff32228e498883fb97320a249b4#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</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: Enable the passing of extra compilation flags, for hardening</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Enable the passing of extra compilation flags, for hardening</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/249</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hisat2.orig/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hisat2/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -176,7 +176,7 @@</span></span>
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<li id="2b2f955d1de9cb2d63191eb231f921af08889937">
<a href="https://salsa.debian.org/med-team/hisat2/-/commit/2ad3dc9b705b8ff32228e498883fb97320a249b4#2b2f955d1de9cb2d63191eb231f921af08889937"><strong>debian/patches/reproducibile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: Make build reproducible</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Make build reproducible</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/250</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hisat2.orig/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hisat2/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -26,7 +26,7 @@</span></span>
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<a href="https://salsa.debian.org/med-team/hisat2/-/commit/2ad3dc9b705b8ff32228e498883fb97320a249b4#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: use the simde header library for greater compatibility</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: use the simde header library for greater compatibility</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/DaehwanKimLab/hisat2/pull/251</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hisat2.orig/aligner_sw.h</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hisat2/aligner_sw.h</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -66,11 +66,1<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -66,11 +66,1<span class="idiff left right">2</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> #define INLINE_CUPS</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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10
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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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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse2.h></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;">+#if defined(__VEC__) && defined(__ALTIVEC__) && !defined(__APPLE_ALTIVEC__)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# undef vector</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# undef pixel</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# undef bool</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> #include <stdint.h></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> #include <iostream></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> #include <limits></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,17 +19,12 @@ Description: use the simde header library for greater compatibility</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> #include "ds.h"</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hisat2.orig/sse_util.h</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hisat2/sse_util.h</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -20,11 +20,1<span class="idiff left right">8</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -20,11 +20,1<span class="idiff left right">3</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> #ifndef SSE_UTIL_H_</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> #define SSE_UTIL_H_</span>
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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"><span class="gi" style="color: #000; background-color: #dfd;">+#define SIMDE_ENABLE_NATIVE_ALIASES</span></span>
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31
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <simde/x86/sse2.h></span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if defined(__VEC__) && defined(__ALTIVEC__) && !defined(__APPLE_ALTIVEC__)</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# undef vector</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# undef pixel</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;">+# undef bool</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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37
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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38
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> #include "assert_helpers.h"</span>
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39
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> #include "ds.h"</span>
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