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<h3>
Dylan Aïssi pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/fastp">Debian Med / fastp</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/fastp/-/commit/7e199d9ed5dd4ba5a46ce6ed0937dba0d261a862">7e199d9e</a></strong>
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<span>by Dylan Aïssi</span>
<i>at 2021-12-07T22:34:20+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.23.2+dfsg</pre>
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<h4>3 changed files:</h4>
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<a href="#742351309009b70e28c04c50b75d5287975926bb">
src/common.h
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<a href="#8f848fe3bda53a34670cfd820d42d2e80c6a1baf">
src/peprocessor.cpp
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<a href="#57c3c58e9b5fb7fc752c23a0041722bf1cf56a8c">
src/read.cpp
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<h4>Changes:</h4>
<li id="742351309009b70e28c04c50b75d5287975926bb">
<a href="https://salsa.debian.org/med-team/fastp/-/commit/7e199d9ed5dd4ba5a46ce6ed0937dba0d261a862#742351309009b70e28c04c50b75d5287975926bb"><strong>src/common.h</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef COMMON_H</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define COMMON_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FASTP_VER "0.23.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FASTP_VER "0.23.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _DEBUG false</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/fastp/-/commit/7e199d9ed5dd4ba5a46ce6ed0937dba0d261a862#8f848fe3bda53a34670cfd820d42d2e80c6a1baf"><strong>src/peprocessor.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="923" 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">@@ -923,8 +923,8 @@ void PairEndProcessor::interleavedReaderTask()</td>
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923
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923
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="cpp"> <span class="n" style="color: #333;">mRightPackReadCounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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924
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="cpp"></span>
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//re-initialize data for next pack</span></span>
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">Read</span></span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">dataLeft</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">*</span><span class="p">[</span><span class="n" style="color: #333;">PACK_SIZE</span><span class="p">];</span></span>
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927
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">Read</span></span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">dataRight</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">*</span><span class="p">[</span><span class="n" style="color: #333;">PACK_SIZE</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">dataLeft</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">*</span><span class="p">[</span><span class="n" style="color: #333;">PACK_SIZE</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="n" style="color: #333;">dataRight</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">*</span><span class="p">[</span><span class="n" style="color: #333;">PACK_SIZE</span><span class="p">];</span></span>
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928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">dataLeft</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">PACK_SIZE</span><span class="p">);</span></span>
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929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">dataRight</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">PACK_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if the consumer is far behind this producer, sleep and wait to limit memory usage</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="961" 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">@@ -961,10 +961,17 @@ void PairEndProcessor::interleavedReaderTask()</td>
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mOptions</span><span class="o" style="font-weight: 600;">-></span><span class="kr" style="font-weight: 600;">thread</span><span class="p">;</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="cpp"> <span class="n" style="color: #333;">mLeftInputLists</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setProducerFinished</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="n" style="color: #333;">mRightInputLists</span><span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setProducerFinished</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mOptions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"> <span class="n" style="color: #333;">loginfo</span><span class="p">(</span><span class="s" style="color: #d14;">"interleaved: loading completed with "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">mLeftPackReadCounter</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" packs"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">mLeftReaderFinished</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">mRightReaderFinished</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mOptions</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC967" class="line" lang="cpp"> <span class="n" style="color: #333;">loginfo</span><span class="p">(</span><span class="s" style="color: #d14;">"Reads loading: completed"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if the last data initialized is not used, free it</span></span>
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dataLeft</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/fastp/-/commit/7e199d9ed5dd4ba5a46ce6ed0937dba0d261a862#57c3c58e9b5fb7fc752c23a0041722bf1cf56a8c"><strong>src/read.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "read.h"</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstring></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "util.h"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Read</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">quality</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">phred64</span><span class="p">){</span></span>
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