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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spoa/-/commit/d435cde5c792e3dad988606ae8d57bda93a9babb">d435cde5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2020-04-13T18:40:17+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.0.2</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#5b11ed83019dc2479735a42da7b6c9eeb7155c33">
src/graph.cpp
</a>
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<li class="file-stats">
<a href="#b958235ee8db37bcaceda04b6d55553b450c2db4">
src/main.cpp
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/d435cde5c792e3dad988606ae8d57bda93a9babb#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">compiler</span><span class="pi">:</span></span>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/spoa/-/commit/d435cde5c792e3dad988606ae8d57bda93a9babb#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,9 +14,12 @@ set(CMAKE_CXX_EXTENSIONS OFF)</td>
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14
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
15
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>spoa_build_executable <span class="s2" style="color: #d14;">"Build spoa standalone tool"</span> OFF<span class="p">)</span></span>
</pre>
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16
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<td class="diff-line-num new_line" data-linenumber="16" 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="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>spoa_build_tests <span class="s2" style="color: #d14;">"Build spoa unit tests"</span> OFF<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>spoa_optimize_for_native <span class="s2" style="color: #d14;">"Buiold spoa with march=native"</span> ON<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="18" 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="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>spoa_optimize_for_native <span class="s2" style="color: #d14;">"Build spoa with -march=native"</span> ON<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="18" 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="18" 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="LC18" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>spoa_optimize_for_portability <span class="s2" style="color: #d14;">"Build spoa with -msse4.1"</span> OFF<span class="p">)</span></span>
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18
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cmake"></span>
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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>spoa_optimize_for_native<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>spoa_optimize_for_portability<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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="LC21" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -msse4.1"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">elseif</span> <span class="p">(</span>spoa_optimize_for_native<span class="p">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -march=native"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" 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="LC25" class="line" lang="cmake"></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/d435cde5c792e3dad988606ae8d57bda93a9babb#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -161,7 +161,7 @@ On the other hand, if you are using `cmake` you can add spoa to your project by</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contact information</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="markdown">For additional information, help and bug reports please send an email to: robert.vaser@fer.hr.</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown">For additional information, help and bug reports please send an email to: robert.vaser@fer.hr<span class="idiff left right">, mile.sikic@fer.hr</span>.</span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Acknowledgement</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/d435cde5c792e3dad988606ae8d57bda93a9babb#5b11ed83019dc2479735a42da7b6c9eeb7155c33"><strong>src/graph.cpp</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">@@ -726,6 +726,8 @@ void Graph::print_dot(const std::string& path) const {</td>
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Graph</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">clear</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"> <span class="n" style="color: #333;">num_codes_</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"> <span class="n" style="color: #333;">num_sequences_</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fill</span><span class="p">(</span><span class="n" style="color: #333;">coder_</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">coder_</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fill</span><span class="p">(</span><span class="n" style="color: #333;">decoder_</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">decoder_</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="cpp"> <span class="n" style="color: #333;">nodes_</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/spoa/-/commit/d435cde5c792e3dad988606ae8d57bda93a9babb#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</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">@@ -10,7 +10,7 @@</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "spoa/spoa.hpp"</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "bioparser/bioparser.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.0.<span class="idiff left right">1</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v3.0.<span class="idiff left right">2</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"algorithm"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">},</span></span>
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