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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49">e23c8f36</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-11-14T19:24:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Series of updates.
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#0077a2c2838f7524dc36a2824fe4af986d35f032">
<span class="new-file">
+
debian/patches/collectionsAbc.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#333a54de40ab446edec11244bdeafa389acd6fdb">
<span class="new-file">
+
debian/patches/hts_nim_tools.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#a2272093ba01901768b56d382ba627f1a24b1f0e">
<span class="new-file">
+
debian/patches/pytest2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#db5264a5b46a8e73e75cc06577624455747ae412">
<span class="new-file">
+
debian/patches/pythonpaths.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" 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="45" 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">@@ -45,7 +45,6 @@ convinced that this is no longer required.</td>
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<td class="diff-line-num old_line" data-linenumber="45" 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">
45
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<td class="diff-line-num new_line" data-linenumber="45" 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">
45
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC45" class="line" lang="mosel"><span class="s1" style="color: #d14;"> #py # conda-specific</span></span>
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<td class="diff-line-num old_line" data-linenumber="46" 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">
46
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<td class="diff-line-num new_line" data-linenumber="46" 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">
46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="mosel"><span class="s1" style="color: #d14;"> python-dateutil >=2.5.0 # likely obsolete?</span></span>
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<td class="diff-line-num old_line" data-linenumber="47" 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">
47
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<td class="diff-line-num new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="mosel"><span class="s1" style="color: #d14;"> pyyaml https://pyyaml.org/wiki/PyYAML</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="48" 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">
48
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<td class="diff-line-num new_line old" data-linenumber="48" 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">
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="mosel"><span class="s1" style="color: #d14;"> python3-seqcluster # to be reuploaded</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="49" 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">
49
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<td class="diff-line-num new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="mosel"><span class="s1" style="color: #d14;"> To be packaged</span></span>
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<td class="diff-line-num old_line" data-linenumber="50" 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">
50
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<td class="diff-line-num new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="mosel"><span class="s1" style="color: #d14;"> fadapa https://github.com/fadapa/fadapa</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="51" 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">
51
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<td class="diff-line-num new_line" data-linenumber="50" 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">
50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="mosel"><span class="s1" style="color: #d14;"> pycrypto</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="82" 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="81" 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">@@ -82,7 +81,7 @@ convinced that this is no longer required.</td>
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<td class="diff-line-num old_line" data-linenumber="82" 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">
82
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<td class="diff-line-num new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;"> pyvcf</span></span>
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<td class="diff-line-num old_line" data-linenumber="83" 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">
83
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="mosel"><span class="s1" style="color: #d14;"> requests</span></span>
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84
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel"><span class="s1" style="color: #d14;"> scipy >=1.3.0</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="mosel"><span class="s1" style="color: #d14;"> seqcluster</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" 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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<pre style="margin: 0;">+<span id="LC84" class="line" lang="mosel"><span class="s1" style="color: #d14;"> seqcluster<span class="idiff left right"> (python3-seqcluster)</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="86" 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">
86
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="mosel"><span class="s1" style="color: #d14;"> statsmodels</span></span>
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<td class="diff-line-num old_line" data-linenumber="87" 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">
87
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="mosel"><span class="s1" style="color: #d14;"> tabulate</span></span>
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<td class="diff-line-num old_line" data-linenumber="88" 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">
88
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="mosel"><span class="s1" style="color: #d14;"> toolz</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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="118" 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">@@ -119,27 +118,14 @@ package python-seqcluster (to be reuploaded)</td>
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<td class="diff-line-num old_line" data-linenumber="119" 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">
119
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages presumed easy to package</span></span>
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<td class="diff-line-num old_line" data-linenumber="120" 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">
120
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<td class="diff-line-num new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------</span></span>
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<td class="diff-line-num old_line" data-linenumber="121" 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">
121
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="mosel"></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="mosel"><span class="s1" style="color: #d14;">package hts_nim_tools</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/brentp/hts-nim-tools</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Likely addressed with the other efforts on nim behind mosdepth</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="mosel"><span class="s1" style="color: #d14;"> salsa</span></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="mosel"></span>
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128
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="mosel"><span class="s1" style="color: #d14;">package "asl solver"</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://www.ampl.com/netlib/ampl/solvers.tgz</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by gjh_asl_json</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="mosel"><span class="s1" style="color: #d14;">r-bioc-HTSFilter</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://bioconductor.org/packages/release/bioc/html/HTSFilter.html</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by seqcluster</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needs r-bioc-edger and r-bioc-deseq (also deseq2) as build dependends which are not in Debian </span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="mosel"><span class="s1" style="color: #d14;">r-bioc-DEGreport</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://bioconductor.org/packages/release/bioc/html/DEGreport.html</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by seqcluster</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needs r-bioc-edger and other dependencies which are not in Debian </span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages of importance for basic NGS workflows with motivation beyond bcbio</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------------------------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" 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="138" 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">@@ -152,13 +138,6 @@ package optitype</td>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/optitype (rudimentary)</span></span>
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<td class="diff-line-num old_line" data-linenumber="153" 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="LC139" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Stuck over too many dependencies</span></span>
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154
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="mosel"></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="mosel"><span class="s1" style="color: #d14;">package vcfanno</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/vcfanno</span></span>
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<td class="diff-line-num old old_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Not fun because of many GO packages that are still missing,</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="mosel"><span class="s1" style="color: #d14;"> "biogo" being one of them.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Stuck over too many dependencies</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="mosel"></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="162" 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">
162
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="mosel"></span>
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163
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="mosel"><span class="s1" style="color: #d14;">Difficult to package to the degree that one is tempted to use conda for the meantime</span></span>
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<td class="diff-line-num old_line" data-linenumber="164" 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">
164
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="mosel"><span class="s1" style="color: #d14;">------------------------------------------------------------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" 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="174" 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">@@ -195,13 +174,6 @@ package sailfish</td>
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195
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/sailfish</span></span>
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<td class="diff-line-num old_line" data-linenumber="196" 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">
196
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="mosel"><span class="s1" style="color: #d14;"> FTBFS</span></span>
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197
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="mosel"><span class="s1" style="color: #d14;">package vt</span></span>
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<td class="diff-line-num old old_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/atks/vt</span></span>
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<td class="diff-line-num old old_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="mosel"><span class="s1" style="color: #d14;">package Rmath</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/atks/Rmath</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by vt</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="mosel"></span>
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205
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="mosel"><span class="s1" style="color: #d14;">package fgbio</span></span>
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<td class="diff-line-num old_line" data-linenumber="206" 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">
206
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<td class="diff-line-num new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/fulcrumgenomics/fgbio</span></span>
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<td class="diff-line-num old_line" data-linenumber="207" 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">
207
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<td class="diff-line-num new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Anyone much into scala?</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49#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">@@ -22,15 +22,23 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> python3-joblib,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># for testing</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> atropos <!nocheck>,</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> bcftools <!nocheck>,</span>
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25
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> bedtools <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> biobambam2 <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> bowtie2 <!nocheck>,</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> cnvkit <!nocheck>,</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> fastqc <!nocheck>,</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> freebayes <!nocheck>,</span>
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27
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> gffread <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> grabix <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> hisat2 <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> hts-nim-tools <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> mosdepth <!nocheck>,</span>
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31
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> multiqc <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> perl <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> libpicard-java <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> libvcflib-tools <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> picard-tools <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> python3-biopython <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> python3-cyvcf2 <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> python3-geneimpacts <!nocheck>,</span>
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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">@@ -39,14 +47,26 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> python3-requests <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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41
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> python3-pytest-mock <!nocheck>,</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> bcftools <!nocheck>,</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> python3-seqcluster <!nocheck>,</span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> pythonpy <!nocheck>,</span>
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> rapmap <!nocheck>,</span>
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43
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<td class="diff-line-num new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> rna-star <!nocheck>,</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> r-other-wasabi <!nocheck>,</span>
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<td class="diff-line-num new new_line" data-linenumber="55" 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">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> r-bioc-htsfilter <!nocheck>,</span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> r-bioc-degreport <!nocheck>,</span>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> r-cran-tidyverse <!nocheck>,</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> r-bioc-tximport <!nocheck>,</span>
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<td class="diff-line-num old_line" data-linenumber="44" 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">
44
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> salmon <!nocheck>,</span>
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<td class="diff-line-num old_line" data-linenumber="45" 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">
45
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> samblaster <!nocheck>,</span>
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<td class="diff-line-num old_line" data-linenumber="46" 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">
46
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<td class="diff-line-num new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> samtools <!nocheck>,</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> seqan-apps <!nocheck>,</span>
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<td class="diff-line-num old_line" data-linenumber="47" 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">
47
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<td class="diff-line-num new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> seqtk <!nocheck>,</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> subread <!nocheck>,</span>
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48
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> tabix <!nocheck>,</span>
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<td class="diff-line-num old_line" data-linenumber="49" 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">
49
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<td class="diff-line-num new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> tophat-recondition <!nocheck>,</span>
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<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> umis <!nocheck>,</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> vcfanno <!nocheck>,</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> vt <!nocheck>,</span>
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50
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"> wham-align <!nocheck>,</span>
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<td class="diff-line-num old_line" data-linenumber="51" 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">
51
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"> xonsh <!nocheck>,</span>
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52
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"># documentation</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" 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="94" 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">@@ -74,6 +94,7 @@ Depends: ${python3:Depends},</td>
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74
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> python3-six,</span>
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75
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> python3-tornado</span>
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76
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">Recommends:</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> cnvkit,</span>
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<td class="diff-line-num old_line" data-linenumber="77" 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">
77
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<td class="diff-line-num new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"> mosdepth,</span>
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<td class="diff-line-num old_line" data-linenumber="78" 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">
78
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<td class="diff-line-num new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> multiqc,</span>
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<td class="diff-line-num old_line" data-linenumber="79" 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">
79
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<td class="diff-line-num new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> python3-arrow,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="83" 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="104" 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">@@ -83,6 +104,8 @@ Recommends:</td>
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83
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"> python3-seqcluster,</span>
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84
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"> python3-statsmodels,</span>
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<td class="diff-line-num old_line" data-linenumber="85" 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">
85
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<td class="diff-line-num new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"> python3-tabulate,</span>
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<td class="diff-line-num new old_line" data-linenumber="86" 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="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> seqan-apps,</span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> vcfanno,</span>
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86
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<td class="diff-line-num new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> vt</span>
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<td class="diff-line-num old_line" data-linenumber="87" 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">
87
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<td class="diff-line-num new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext">Suggests:</span>
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88
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<td class="diff-line-num new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="plaintext"> bcbio-doc,</span>
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<li id="0077a2c2838f7524dc36a2824fe4af986d35f032">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49#0077a2c2838f7524dc36a2824fe4af986d35f032"><strong>debian/patches/collectionsAbc.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/bcbio/utils.py</span></span>
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2
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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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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/bcbio/utils.py</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/bcbio/utils.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -19,7 +19,8 @@</span> import six</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> import toolz as tz</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> import yaml</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from collections import Mapping, OrderedDict</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from collections.abc import Mapping</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from collections import OrderedDict</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"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> try:</span></pre>
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<li id="333a54de40ab446edec11244bdeafa389acd6fdb">
<a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49#333a54de40ab446edec11244bdeafa389acd6fdb"><strong>debian/patches/hts_nim_tools.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/bcbio/bam/readstats.py</span></span>
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2
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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;">--- bcbio.orig/bcbio/bam/readstats.py</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/bcbio/bam/readstats.py</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -89,7 +89,7 @@</span> def number_of_mapped_reads(data, bam_fil</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> bam.index(bam_file, data["config"], check_timestamp=False)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> num_cores = dd.get_num_cores(data)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> with file_transaction(data, count_file) as tx_out_file:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cmd = ("hts_nim_tools count-reads -t {num_cores} -F {flag} {bed_file} {bam_file} > {tx_out_file}")</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = ("hts-nim-tools count-reads -t {num_cores} -F {flag} {bed_file} {bam_file} > {tx_out_file}")</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> do.run(cmd.format(**locals()), "Count mapped reads: %s" % (dd.get_sample_name(data)))</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> count = 0</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> with open(count_file) as in_handle:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/docs/contents/internals.md</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/docs/contents/internals.md</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/docs/contents/internals.md</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -137,8 +137,8 @@</span> resources:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> 1. hts_nim counts:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> ```shell</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hts_nim_tools count-reads -t 16 -F 1804 /path/samplex/counts/fullgenome.bed samplex-sort-cumi.bam > fullgenome-1804-counts.txt</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hts_nim_tools count-reads -t 16 -F 1804 cleaned-target.bed samplex-sort-cumi.bam > cleaned-target-merged-1804-counts.txt</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hts-nim-tools count-reads -t 16 -F 1804 /path/samplex/counts/fullgenome.bed samplex-sort-cumi.bam > fullgenome-1804-counts.txt</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hts-nim-tools count-reads -t 16 -F 1804 cleaned-target.bed samplex-sort-cumi.bam > cleaned-target-merged-1804-counts.txt</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> ```</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> 1. samtools read statistics::</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> ```shell</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49#a2272093ba01901768b56d382ba627f1a24b1f0e"><strong>debian/patches/pytest2to3.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: bcbio/tests/run_tests.sh</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;">--- bcbio.orig/tests/run_tests.sh</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;">+++ bcbio/tests/run_tests.sh</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -30,4 +30,4 @@</span> export PYTHONNOUSERSITE=1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> if [ -d "../bcbio/pipeline" ]; then</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> [ -f ../bcbio/pipeline/version.py ] || touch ../bcbio/pipeline/version.py</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-"$BCBIO_DIR/py.test" -p no:cacheprovider -p no:stepwise -v -s -m ${MARK} "$@"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+py.test-3 -p no:cacheprovider -p no:stepwise -v -s -m ${MARK} "$@"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49#db5264a5b46a8e73e75cc06577624455747ae412"><strong>debian/patches/pythonpaths.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: bcbio/scripts/bcbio_fastq_umi_prep.py</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;">--- bcbio.orig/scripts/bcbio_fastq_umi_prep.py</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;">+++ bcbio/scripts/bcbio_fastq_umi_prep.py</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 python</span></span>
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7
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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/python3</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> """Convert fastq inputs into paired inputs with UMIs in read names.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> Handles three cases:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/scripts/bcbio_nextgen_install.py</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/scripts/bcbio_nextgen_install.py</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/scripts/bcbio_nextgen_install.py</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> """Automatically install required tools and data to run bcbio-nextgen pipelines.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> This automates the steps required for installation and setup to make it easier to get started with</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/scripts/bcbio_nextgen.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/scripts/bcbio_nextgen.py</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/scripts/bcbio_nextgen.py</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python -Es</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -s</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> """Run an automated analysis pipeline for high throughput sequencing data.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> Handles runs in local or distributed mode based on the command line or</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/scripts/bcbio_setup_genome.py</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/scripts/bcbio_setup_genome.py</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/scripts/bcbio_setup_genome.py</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python -Es</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3 -Es</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> Script to set up a custom genome for bcbio-nextgen</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/scripts/cwl/arvados_bcbio_runtimes.py</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/scripts/cwl/arvados_bcbio_runtimes.py</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/scripts/cwl/arvados_bcbio_runtimes.py</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> """Summarize runtimes for bcbio Arvados CWL runs.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> Usage:</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/scripts/cwltool2wdl.py</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/scripts/cwltool2wdl.py</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/scripts/cwltool2wdl.py</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> """Exploratory code to convert bcbio generated CWL into WDL.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> Uses cwltool parser to parse input CWL then, calls out to cwl2wdl</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcbio/tests/run_tests.sh</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcbio.orig/tests/run_tests.sh</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcbio/tests/run_tests.sh</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="p">@@ -24,7 +24,8 @@</span> else</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> unset PYTHONHOME</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-unset PYTHONPATH</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+export PATH=$(pwd)/scripts:$PATH</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+export PYTHONPATH=$(pwd)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> export PYTHONNOUSERSITE=1</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> # Ensure version.py exists in raw cloned bcbio directory</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> if [ -d "../bcbio/pipeline" ]; then</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/-/commit/e23c8f362fb33cc9a54dd755e132f2c961ca6d49#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#spelling</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">pytest2to3.patch</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">include_tests</span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">#add_installed_dir_paths.patch</span>
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4
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">do_not_use_git.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">pythonpaths.patch</span>
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<td class="diff-line-num new old_line" data-linenumber="5" 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="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">hts_nim_tools.patch</span>
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<td class="diff-line-num new old_line" data-linenumber="5" 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="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">collectionsAbc.patch</span></pre>
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