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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/paleomix">Debian Med / paleomix</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/commit/95b58c29dbf3bf4e8a0731f388951e085342faa6">95b58c29</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T09:21:12Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.13.4</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#e321de7670047f8a17ca0621f4e85c596f2a665d">
docs/phylo_pipeline/usage.rst
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<li class="file-stats">
<a href="#82233c75268e15a595a90e8494933e20039bfa91">
paleomix/nodes/picard.py
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<li class="file-stats">
<a href="#b495d03fad7939deb535f23f37c46d1373a66724">
paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml
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</li>
</ul>
<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/paleomix/commit/95b58c29dbf3bf4e8a0731f388951e085342faa6#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changelog</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.4] - 2019-03-25</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p"> -</span> Improved detection of Picard versions in cases where 'java'</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"> outputs additional text.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.3] - 2018-11-01</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p"> -</span> Fixed validation/read counting of pre-trimmed reads not including</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="581" 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="587" 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">@@ -581,7 +587,8 @@ the (partially) updated documentation now hosted on ReadTheDocs.</td>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="markdown"><span class="p"> -</span> Switching to more traditional version-number tracking.</span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
584
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Unreleased</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...HEAD</span></span>
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<td class="diff-line-num new new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Unreleased</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.4...HEAD</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.4</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...v1.2.13.4</span></span>
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585
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<td class="diff-line-num new_line" data-linenumber="592" 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">
592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.3</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3</span></span>
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<td class="diff-line-num old_line" data-linenumber="586" 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">
586
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593
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.2</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2</span></span>
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587
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<td class="diff-line-num new_line" data-linenumber="594" 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">
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.1</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13...v1.2.13.1</span></span>
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<li id="e321de7670047f8a17ca0621f4e85c596f2a665d">
<a href="https://salsa.debian.org/med-team/paleomix/commit/95b58c29dbf3bf4e8a0731f388951e085342faa6#e321de7670047f8a17ca0621f4e85c596f2a665d"><strong>docs/phylo_pipeline/usage.rst</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">@@ -22,15 +22,15 @@ To execute the pipeline, a command corresponding to the step to be invoked is us</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Samples</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">-------</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">The phylogenetic pipeline expects a number of samples to be specified. Each sample has a name, a <span class="idiff left right">gender</span>, and a genotyping method::</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">The phylogenetic pipeline expects a number of samples to be specified. Each sample has a name, a <span class="idiff left right">sex</span>, and a genotyping method::</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> Samples:</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> <GROUP>:</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> SAMPLE_NAME:</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> <span class="idiff left right">Gender</span>: ...</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> <span class="idiff left right">Sex</span>: ...</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> Genotyping Method: ...</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"><span class="idiff left right">Gender</span> is required, and is used to filter SNPs at homozygous sex chromsomes (e.g. chrX and chrY for male humans). Any names may be used, and can simply be set to e.g. 'NA' in case this feature is not used.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"><span class="idiff left right">Sex</span> is required, and is used to filter SNPs at homozygous sex chromsomes (e.g. chrX and chrY for male humans). Any names may be used, and can simply be set to e.g. 'NA' in case this feature is not used.</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">The genotyping method is either "SAMTools" for the default genotyping procedure using samtools mpileupe | bcftools view, or "Random Sampling" to sample one random nucleotide in the pileup at each position. This key may be left out to use the default (SAMTools) method.</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/paleomix/commit/95b58c29dbf3bf4e8a0731f388951e085342faa6#82233c75268e15a595a90e8494933e20039bfa91"><strong>paleomix/nodes/picard.py</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">@@ -239,7 +239,7 @@ def picard_command(config, command):</td>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">requirement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Requirement</span><span class="p">(</span><span class="n" style="color: #333;">call</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">finalized_call</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Picard tools"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">search</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">r"<span class="idiff left right">^(\d+)\.(\d+)</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">search</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">r"<span class="idiff left right">\b(\d+)\.(\d+)\.\d+</span>"</span><span class="p">,</span></span>
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243
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243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">checks</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">versions</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">GE</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">137</span><span class="p">))</span></span>
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">_PICARD_VERSION_CACHE</span><span class="p">[</span><span class="n" style="color: #333;">jar_path</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">requirement</span></span>
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/paleomix/commit/95b58c29dbf3bf4e8a0731f388951e085342faa6#b495d03fad7939deb535f23f37c46d1373a66724"><strong>paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml</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">@@ -8,25 +8,25 @@ Project:</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># in 'ExcludeSamples' and 'FilterSingletons'.</span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">Samples</span><span class="pi">:</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">06_3928A</span><span class="pi">:</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">DDR7602</span><span class="pi">:</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">LBUS5</span><span class="pi">:</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">M-0182896</span><span class="pi">:</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">NL07434</span><span class="pi">:</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">P13527</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">P13626</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">P17777</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">Pi1845A</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">Pi1889</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Gender</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">Sex</span></span><span class="pi">:</span> <span class="s" style="color: #d14;">NA</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Specifies a set of regions of interest, each representing one or more</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># named regions in a reference sequence (e.g. genes) in BED format.</span></span>
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