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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/racon">Debian Med / racon</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/racon/-/commit/683c68cfacfeb310b06c6b172bbf49266d7c104e">683c68cf</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-09-01T17:17:12+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.4.21</pre>
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<h4>3 changed files:</h4>
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<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#a5a7b76c67b308f1d3ac8995827cde0ee87db68e">
src/polisher.cpp
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<li class="file-stats">
<a href="#693654edd1082408d152bbeaa3b25a7424a0b8b5">
test/racon_test.cpp
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/racon/-/commit/683c68cfacfeb310b06c6b172bbf49266d7c104e#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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1
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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 3.2<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>racon<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_version 1.4.2<span class="idiff left right">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>racon_version 1.4.2<span class="idiff left right">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_ARCHIVE_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/lib<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_LIBRARY_OUTPUT_DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">PROJECT_BINARY_DIR</span><span class="si" style="color: #d14;">}</span>/lib<span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/racon/-/commit/683c68cfacfeb310b06c6b172bbf49266d7c104e#a5a7b76c67b308f1d3ac8995827cde0ee87db68e"><strong>src/polisher.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="299" 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="299" 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">@@ -299,7 +299,7 @@ void Polisher::initialize() {</td>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">><span class="idiff left right">=</span></span> <span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">overlaps</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<li id="693654edd1082408d152bbeaa3b25a7424a0b8b5">
<a href="https://salsa.debian.org/med-team/racon/-/commit/683c68cfacfeb310b06c6b172bbf49266d7c104e#693654edd1082408d152bbeaa3b25a7424a0b8b5"><strong>test/racon_test.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">@@ -233,13 +233,13 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualities) {</td>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC234" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">polished_sequences</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="n" style="color: #333;">polish</span><span class="p">(</span><span class="n" style="color: #333;">polished_sequences</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">polished_sequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;"><span class="idiff left right">39</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">polished_sequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;"><span class="idiff left right">40</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">total_length</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="LC239" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">polished_sequences</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">total_length</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">total_length</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">389394</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">total_length</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">401246</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualitiesFull</span><span class="p">)</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">@@ -444,13 +444,13 @@ TEST_F(RaconPolishingTest, FragmentCorrectionWithQualitiesCUDA) {</td>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC445" 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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">racon</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Sequence</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">polished_sequences</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp"> <span class="n" style="color: #333;">polish</span><span class="p">(</span><span class="n" style="color: #333;">polished_sequences</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">polished_sequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;"><span class="idiff left right">39</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">polished_sequences</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="mi" style="color: #099;"><span class="idiff left right">40</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">total_length</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="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">polished_sequences</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> <span class="n" style="color: #333;">total_length</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">().</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">total_length</span><span class="p">,</span> <span class="mi" style="color: #099;">3<span class="idiff left right">85543</span></span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// CPU 389394</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPECT_EQ</span><span class="p">(</span><span class="n" style="color: #333;">total_length</span><span class="p">,</span> <span class="mi" style="color: #099;">3<span class="idiff left right">97185</span></span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// CPU 389394</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"><span class="n" style="color: #333;">TEST_F</span><span class="p">(</span><span class="n" style="color: #333;">RaconPolishingTest</span><span class="p">,</span> <span class="n" style="color: #333;">FragmentCorrectionWithQualitiesFullCUDA</span><span class="p">)</span> <span class="p">{</span></span>
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