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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/diamond-aligner">Debian Med / diamond-aligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/commit/c8961dd6ee70bd172eb185ce7af337f19feecb49">c8961dd6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-01T12:55:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build issue fixed by upstream commit
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/commit/8a9614b33bbd9940720b5a0a9bed3eca5328bfd9">8a9614b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-01T13:00:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop unneeded paragraph from d/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/diamond-aligner/commit/0ce1d6b30077b33d8db9b51fcceb104a98d49694">0ce1d6b3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-01T13:02:36Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#7504edb146624613085f847641b8908c861bf3ee">
<span class="new-file">
+
debian/patches/82feea2aee5c82e283704b9317cb5e8abc625f90.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/diamond-aligner/compare/2ff71e00a1b589ddd4dd6097a028704e85de824a...0ce1d6b30077b33d8db9b51fcceb104a98d49694#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">diamond-aligner (0.9.25+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">diamond-aligner (0.9.25+dfsg-1) <span class="idiff left right">unstable</span>; 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"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> TODO: Build issue see</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> https://github.com/bbuchfink/diamond/issues/295</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Drop unneeded paragraph from d/copyright</span>
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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="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 31 Jul 2019 14:57:15</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 01 Aug 2019 15:00:33</span> +0200</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">diamond-aligner (0.9.24+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/diamond-aligner/compare/2ff71e00a1b589ddd4dd6097a028704e85de824a...0ce1d6b30077b33d8db9b51fcceb104a98d49694#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,29 +9,6 @@ Files: *</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Copyright: 2014-2016, University of Tuebingen, Benjamin Buchfink</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">License: BSD-3-clause</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">Files: src/util/fast_mutex.h</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> src/util/tinythread.*</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Copyright: 2010-2012 Marcus Geelnard</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">License: as-is</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> This software is provided 'as-is', without any express or implied</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> warranty. In no event will the authors be held liable for any damages</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> arising from the use of this software.</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> Permission is granted to anyone to use this software for any purpose,</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> including commercial applications, and to alter it and redistribute it</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> freely, subject to the following restrictions:</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> 1. The origin of this software must not be misrepresented; you must not</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> claim that you wrote the original software. If you use this software</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> in a product, an acknowledgment in the product documentation would be</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> appreciated but is not required.</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> 2. Altered source versions must be plainly marked as such, and must not be</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> misrepresented as being the original software.</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> 3. This notice may not be removed or altered from any source</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> distribution.</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Files: debian/*</span>
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36
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Copyright: 2016 Andreas Tille <tille@debian.org></span>
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37
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: BSD-3-clause</span>
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<li id="7504edb146624613085f847641b8908c861bf3ee">
<a href="https://salsa.debian.org/med-team/diamond-aligner/compare/2ff71e00a1b589ddd4dd6097a028704e85de824a...0ce1d6b30077b33d8db9b51fcceb104a98d49694#7504edb146624613085f847641b8908c861bf3ee"><strong>debian/patches/82feea2aee5c82e283704b9317cb5e8abc625f90.patch</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 82feea2aee5c82e283704b9317cb5e8abc625f90 Mon Sep 17 00:00:00 2001</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">From: Benjamin Buchfink <buchfink@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Date: Thu, 1 Aug 2019 14:36:14 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Subject: [PATCH] Fixed #295.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> src/dp/needleman_wunsch.cpp | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 1 file changed, 1 insertion(+), 1 deletion(-)</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">diff --git a/src/dp/needleman_wunsch.cpp b/src/dp/needleman_wunsch.cpp</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">index abb47bb..2050eea 100644</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/dp/needleman_wunsch.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/dp/needleman_wunsch.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -167,7 +167,7 @@</span> const Fixed_score_buffer<_score>& needleman_wunsch(sequence query, sequence subj</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> return mtx.score_buffer();</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-template const Fixed_score_buffer<int>& needleman_wunsch(sequence query, sequence subject, int &max_score, const Local&, const int&);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// template const Fixed_score_buffer<int>& needleman_wunsch(sequence query, sequence subject, int &max_score, const Local&, const int&);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> int needleman_wunsch(sequence query, sequence subject, int qbegin, int qend, int sbegin, int send, unsigned node, unsigned edge, Diag_graph &diags, bool log)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> {</span></pre>
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<a href="https://salsa.debian.org/med-team/diamond-aligner/compare/2ff71e00a1b589ddd4dd6097a028704e85de824a...0ce1d6b30077b33d8db9b51fcceb104a98d49694#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">avoid_unwanted_optimisation.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">no_march_native.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">82feea2aee5c82e283704b9317cb5e8abc625f90.patch</span></pre>
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