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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/stacks">Debian Med / stacks</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/509bbff5f903b735e12239370a5f582093be83a7">509bbff5</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-04-26T01:39:31+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.53+dfsg</pre>
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<h4>3 changed files:</h4>
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<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
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<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
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scripts/denovo_map.pl
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/stacks/-/commit/509bbff5f903b735e12239370a5f582093be83a7#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">Stacks</span> <span class="m" style="color: #099;">2.53</span> <span class="p">-</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">28</span><span class="p">,</span> <span class="m" style="color: #099;">2020</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="p">----------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"> <span class="n" style="color: #333;">Bugfix</span><span class="p">:</span> <span class="n" style="color: #333;">denovo_map</span><span class="p">.</span><span class="n" style="color: #333;">pl</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">broken</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">running</span> <span class="n" style="color: #333;">cstacks</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">non</span><span class="p">-</span><span class="n" style="color: #333;">genetic</span> <span class="n" style="color: #333;">map</span> <span class="n" style="color: #333;">datasets</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">Stacks</span> <span class="m" style="color: #099;">2.52</span> <span class="p">-</span> <span class="n" style="color: #333;">March</span> <span class="m" style="color: #099;">5</span><span class="p">,</span> <span class="m" style="color: #099;">2020</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="mosel"><span class="p">---------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="mosel"> <span class="n" style="color: #333;">Feature</span><span class="p">:</span> <span class="n" style="color: #333;">denovo_map</span><span class="p">.</span><span class="n" style="color: #333;">pl</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="p">--</span><span class="n" style="color: #333;">resume</span> <span class="k" style="font-weight: 600;">options</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">restart</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">pipeline</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">previous</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">failed</span></span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/509bbff5f903b735e12239370a5f582093be83a7#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</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">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"># Process this file with autoconf to produce a configure script.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">AC_PREREQ(2.59)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.5<span class="idiff left right">2</span>])</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">AC_INIT([Stacks], [2.5<span class="idiff left right">3</span>])</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">AC_CONFIG_AUX_DIR([config])</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_CONFIG_SRCDIR([src/ustacks.cc])</span>
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<a href="https://salsa.debian.org/med-team/stacks/-/commit/509bbff5f903b735e12239370a5f582093be83a7#f80f154b64490a485c4418bd70f94184f6336dce"><strong>scripts/denovo_map.pl</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">@@ -571,8 +571,8 @@ sub parse_population_map {</td>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@k</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="o" style="font-weight: 600;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$pops</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@k</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="nv" style="color: #008080;">$k</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><span class="idiff left">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">parent</span></span><span class="p"><span class="idiff">"</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$k</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">progeny</span></span><span class="p"><span class="idiff">")</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">or</span></span></span>
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$k</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><span class="idiff left">==</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">progent</span></span><span class="p"><span class="idiff">"</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$k</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">==</span></span> <span class="p">"</span><span class="s2" style="color: #d14;">parent</span><span class="p">")</span> <span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="p">(</span><span class="nv" style="color: #008080;">$k</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">eq</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">parent</span></span><span class="p"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$k</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">progeny</span></span><span class="p"><span class="idiff">")</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">||</span></span></span>
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$k</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">eq</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">progeny</span></span><span class="p"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$k</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">eq</span></span> <span class="p">"</span><span class="s2" style="color: #d14;">parent</span><span class="p">")</span> <span class="p">)</span> <span class="p">{</span></span>
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Genetic map detected from population map, only 'parent' samples will be loaded into the catalog.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="perl"> <span class="nv" style="color: #008080;">$$map</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">true</span><span class="p">;</span></span>
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578
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="perl"> <span class="p">}</span></span>
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