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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/spoa">Debian Med / spoa</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/spoa/-/commit/b3265c2c707cad0a3f047f13b23290522c517628">b3265c2c</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-01-08T13:24:45+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.0.6+ds</pre>
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<h4>3 changed files:</h4>
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/b3265c2c707cad0a3f047f13b23290522c517628#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" 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="34" 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">@@ -34,7 +34,7 @@ matrix:</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">eval "${SET_COMPILER}"</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/google/googletest && cd googletest && mkdir build && cd build</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/google/googletest && cd googletest && mkdir build && cd build<span class="idiff left right"> && git checkout 703bd9c</span></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -DCMAKE_CXX_FLAGS="-std=c++11" .. && make && sudo make install</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd ../../</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"></span>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/b3265c2c707cad0a3f047f13b23290522c517628#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 3.9<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>spoa VERSION 4.0.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>spoa VERSION 4.0.<span class="idiff left right">6</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"> LANGUAGES CXX</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"> DESCRIPTION <span class="s2" style="color: #d14;">"Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,7 +61,7 @@ target_include_directories(${PROJECT_NAME} PUBLIC</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cmake"> cereal<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>BUILD_SHARED_LIBS<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span>TARGET <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> PROPERTY SOVERSION <span class="idiff left right">= </span><span class="s2" style="color: #d14;">"7.0.0"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set_property</span><span class="p">(</span>TARGET <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span> PROPERTY SOVERSION <span class="s2" style="color: #d14;">"7.0.0"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span> <span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>spoa_generate_dispatch<span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/b3265c2c707cad0a3f047f13b23290522c517628#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Spoa</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Latest GitHub release</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/release/rvaser/spoa.svg</span><span class="p">)</span>](https://github.com/rvaser/spoa/releases/latest)</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status for gcc/clang</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.<span class="idiff left">org/rvaser/spoa.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.org</span>/rvaser/spoa)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build status for gcc/clang</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.<span class="idiff left">com/rvaser/spoa.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.com</span>/rvaser/spoa)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Published in Genome Research</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/published%20in-Genome%20Research-blue.svg</span><span class="p">)</span>](https://doi.org/10.1101/gr.214270.116)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm (as described in 10.1093/bioinformatics/18.3.452) which is used to generate consensus sequences (as described in 10.1093/bioinformatics/btg109). It supports three alignment modes: local (Smith-Waterman), global (Needleman-Wunsch) and semi-global alignment (overlap), and three gap modes: linear, affine and convex (piecewise affine). It also supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high latency shifts), <span class="p">[</span><span class="nv" style="color: #008080;">SIMDe</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/simd-everywhere/simde</span><span class="p">)</span> and dispatching.</span>
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