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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/stacks">Debian Med / stacks</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/509bbff5f903b735e12239370a5f582093be83a7">509bbff5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-04-26T01:39:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.53+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/d6a65fe55a286d8b8ffdc90b0e0d46998b9972ba">d6a65fe5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-04-26T01:39:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/97e227846ab286d5c11436b5a9c06900c2c2b803">97e22784</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-04-26T01:39:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.53+dfsg'
Update to upstream version '2.53+dfsg'
with Debian dir cf09378c22f5f97fdc9c99c815431a6782a99f47</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/2c62e2d5f3ae0fd5adfbc68f3e58efba359e4e09">2c62e2d5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-04-26T01:45:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/stacks/-/commit/7df2bfc5e945406aceb414a3c25b928aea76c2ed">7df2bfc5</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-04-26T01:57:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Ready to upload.
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#23dca115fb11d8d80d75cc105cbca9aaef0bab81">
<span class="new-file">
+
debian/patches/RisR.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<li class="file-stats">
<a href="#f80f154b64490a485c4418bd70f94184f6336dce">
scripts/denovo_map.pl
</a>
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</ul>
<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#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>
</pre>
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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>
</pre>
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<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#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/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">stacks (2.53+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Updated bio.tools entry to lower-case</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Added dependency on littler to allow execution</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> of R script</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sun, 26 Apr 2020 01:41:49 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">stacks (2.52+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -23,7 +23,8 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> libdbi-perl</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Recommends: libspreadsheet-writeexcel-perl,</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> python3</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> littler</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Conflicts: stacks-web</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Provides: stacks-web</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Replaces: stacks-web</span>
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<a href="https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#23dca115fb11d8d80d75cc105cbca9aaef0bab81"><strong>debian/patches/RisR.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: stacks/scripts/stacks-hist2d-loci-samples-coverage</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- stacks.orig/scripts/stacks-hist2d-loci-samples-coverage</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ stacks/scripts/stacks-hist2d-loci-samples-coverage</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env Rscript</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/r</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> usage = "\</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> usage: stacks-hist2d-loci-samples-coverage reads_per_sample_per_locus.tsv</span></pre>
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<a href="https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">RisR.patch</span>
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1
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">script-exe-paths</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_debian_packaged_htslib.patch</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</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">@@ -19,4 +19,4 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> Entry: stacks</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> - Name: bio.tools</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> Entry: <span class="idiff left right">S</span>tacks</span></pre>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Entry: <span class="idiff left right">s</span>tacks</span></pre>
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<a href="https://salsa.debian.org/med-team/stacks/-/compare/3c13ab827dffd2dbfa6ba26be491f5261e8fe4eb...7df2bfc5e945406aceb414a3c25b928aea76c2ed#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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571
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571
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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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572
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572
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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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573
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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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574
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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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<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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<pre style="margin: 0;"> <span id="LC578" class="line" lang="perl"> <span class="p">}</span></span>
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