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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/berkeley-express">Debian Med / berkeley-express</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/berkeley-express/commit/b0d54647fd82c9bd72ac591a19ae6d3919beb002">b0d54647</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-11-17T15:24:35Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.3+dfsg</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7">
src/CMakeLists.txt
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<li class="file-stats">
<a href="#a719a72887c086505783183adcae66d1c377ee6f">
src/targets.cpp
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/berkeley-express/commit/b0d54647fd82c9bd72ac591a19ae6d3919beb002#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</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">@@ -6,6 +6,9 @@ set(${PROJECT_NAME}_VERSION_MAJOR 1)</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_NAME</span><span class="si" style="color: #d14;">}</span>_VERSION_MINOR 5<span class="p">)</span></span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</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>_VERSION_PATCH 1<span class="p">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"></span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD 11<span class="p">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD_REQUIRED ON<span class="p">)</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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"></span>
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9
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12
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<pre style="margin: 0;"> <span id="LC12" 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;">"-Wall"</span><span class="p">)</span></span>
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10
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS_DEBUG <span class="s2" style="color: #d14;">"-g </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;">"</span><span class="p">)</span></span>
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<li id="631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7">
<a href="https://salsa.debian.org/med-team/berkeley-express/commit/b0d54647fd82c9bd72ac591a19ae6d3919beb002#631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7"><strong>src/CMakeLists.txt</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">@@ -7,7 +7,7 @@ endif(PROTOBUF_FOUND)</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>express <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">sources</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">headers</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROTO_SOURCES</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROTO_HEADERS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">Boost_LIBRARIES</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;"><span class="idiff left">ZLIB_LIBRARIES</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="idiff"> </span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff right">BAMTOOLS</span>_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">Boost_LIBRARIES</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;"><span class="idiff left">BAMTOOLS_LIBRARIES</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="idiff"> </span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff right">ZLIB</span>_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>GPERFTOOLS_TCMALLOC<span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>LIBRARIES <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIBRARIES</span><span class="si" style="color: #d14;">}</span> <span class="s2" style="color: #d14;">"libtcmalloc_minimal.a"</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,9 @@ endif(PROTOBUF_FOUND)</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>WIN32<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>express <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">(</span>WIN32<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">elseif</span><span class="p">(</span>APPLE<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;">target_link_libraries</span><span class="p">(</span>express <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIBRARIES</span><span class="si" style="color: #d14;">}</span> pthread<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">elseif</span><span class="p">(</span>UNIX<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">target_link_libraries</span><span class="p">(</span>express <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">LIBRARIES</span><span class="si" style="color: #d14;">}</span> pthread rt<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span><span class="idiff left right">WIN32</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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="LC28" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">install</span><span class="p">(</span>TARGETS express DESTINATION bin<span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/berkeley-express/commit/b0d54647fd82c9bd72ac591a19ae6d3919beb002#a719a72887c086505783183adcae66d1c377ee6f"><strong>src/targets.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">@@ -113,12 +113,12 @@ double Target::sample_likelihood(bool with_pseudo,</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LOG_1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tot_mass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mass</span><span class="p">(</span><span class="n" style="color: #333;">with_pseudo</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tot_eff_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cached_effective_length</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">lib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">bias_table</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tot_eff_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cached_effective_length</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">static_cast</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bias_table</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">neighbors</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">foreach</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Target</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">neighbor</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">neighbors</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="n" style="color: #333;">tot_mass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_add</span><span class="p">(</span><span class="n" style="color: #333;">tot_mass</span><span class="p">,</span> <span class="n" style="color: #333;">neighbor</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mass</span><span class="p">(</span><span class="n" style="color: #333;">with_pseudo</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">tot_eff_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_add</span><span class="p">(</span><span class="n" style="color: #333;">tot_eff_len</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">neighbor</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cached_effective_length</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">lib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">bias_table</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">neighbor</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cached_effective_length</span><span class="p">(</span><span class="k" style="font-weight: 600;"><span class="idiff left">static_cast</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lib</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">bias_table</span></span><span class="p"><span class="idiff right">)</span>));</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tot_mass</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tot_eff_len</span><span class="p">;</span></span>
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