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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/unanimity">Debian Med / unanimity</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/unanimity/commit/8ac78dda0954c3d1e1b68a255675f0da1a655af0">8ac78dda</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-12-20T07:57:36Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix some issues in gcc9
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<h4>2 changed files:</h4>
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<a href="#20775640da663809ffd0da43d13b36cabd23eb7a">
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+
debian/patches/gcc9.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="20775640da663809ffd0da43d13b36cabd23eb7a">
<a href="https://salsa.debian.org/med-team/unanimity/commit/8ac78dda0954c3d1e1b68a255675f0da1a655af0#20775640da663809ffd0da43d13b36cabd23eb7a"><strong>debian/patches/gcc9.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Fix some issues in gcc-9</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: Thu, 19 Dec 2019 08:14:41 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/src/main/ccs.cpp</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/ccs.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -10,6 +10,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> #include <sstream></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> #include <string></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> #include <vector></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <iomanip></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> #include <boost/algorithm/string.hpp></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> #include <boost/algorithm/string/join.hpp></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -468,7 +469,7 @@</span> static int Runner(const PacBio::CLI::Res</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> std::make_unique<BamWriter>(outputFile, PrepareHeader(args.InputCommandLine(), ds));</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> const string pbiFileName = outputFile + ".pbi";</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> auto ccsPbi = std::make_unique<PbiBuilder>(pbiFileName);</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- writer = async(launch::async, BamWriterThread, ref(workQueue), move(ccsBam), move(ccsPbi),</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ writer = async(launch::async, BamWriterThread, ref(workQueue), std::move(ccsBam), move(ccsPbi),</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> settings);</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> // Always generate pbi file</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -567,8 +568,8 @@</span> static int Runner(const PacBio::CLI::Res</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> chunk->back().Reads.emplace_back(</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> Subread{ReadId(movieNames[movieName], *holeNumber,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> Interval(read.QueryStart(), read.QueryEnd())),</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- read.ReadAccuracy(), SNR(read.SignalToNoise()), move(chem)});</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ read.Sequence(), std::move(ipd), std::move(pw), read.LocalContextFlags(),</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ read.ReadAccuracy(), SNR(read.SignalToNoise()), std::move(chem)});</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> // run the remaining tasks</span></pre>
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<a href="https://salsa.debian.org/med-team/unanimity/commit/8ac78dda0954c3d1e1b68a255675f0da1a655af0#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -3,3 +3,4 @@ git-version.patch</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">no-static-linking.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">do_not_refer_to_non-existing_images.patch</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">gcc9.patch</span></pre>
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