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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/cnvkit">Debian Med / cnvkit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cnvkit/-/commit/5261fdb49808e34e7d0a52d6add855db169f0802">5261fdb4</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:04:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cnvkit/-/commit/8e8e29f523618f5b8e23d86fbed68d43364e4097">8e8e29f5</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:05:03+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cnvkit/-/commit/98e9a90b29bbccbfe367c76aca7f57a006373b0f">98e9a90b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:05:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.9.9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cnvkit/-/commit/5cc7febe4e3b9c6ccd1a0fcb4da3c45b09ab3e84">5cc7febe</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:06:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.9.9'
Update to upstream version '0.9.9'
with Debian dir 0f5ccbd43ac932240a3894782eefe0e9c119bb37</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cnvkit/-/commit/2de423aea0085e98acf39e4537c21141b9f5027b">2de423ae</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:06:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cnvkit/-/commit/93b7f59dc174da24f774c2451a498e3c0a77c580">93b7f59d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:06:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: watch file standard 4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/cnvkit/-/commit/2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e">2ee1721d</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-09-13T19:06:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>29 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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</li>
<li class="file-stats">
<a href="#42d036b285f793fa4706218270f28c4e0af74569">
cnvlib/_version.py
</a>
</li>
<li class="file-stats">
<a href="#0dd6dacf3a32d43e909fde3613a86d002941bcc6">
cnvlib/autobin.py
</a>
</li>
<li class="file-stats">
<a href="#3c97ce14774c9dcaaf77c07a55b41a9bb29613dd">
cnvlib/cnary.py
</a>
</li>
<li class="file-stats">
<a href="#37071ebf7e39e57e21ff893de63e92a9b7f6fcba">
cnvlib/commands.py
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<li class="file-stats">
<a href="#b1c2e997cbcbc150dfbb18cabfe5fbefc6fe41ce">
cnvlib/coverage.py
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<li class="file-stats">
<a href="#62d353493b66e1cacfcb64b472183da221ff7045">
cnvlib/diagram.py
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<li class="file-stats">
<a href="#7b2b1c44e1461bc889009b1993bafbdf3768bc70">
cnvlib/reports.py
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<li class="file-stats">
<a href="#f1f7d899f70bf68ebb7f625ec2ac7532559cd37d">
cnvlib/scatter.py
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</li>
<li class="file-stats">
<a href="#f7b099f991a0340c6329ac46493597d82cfb8402">
cnvlib/segmentation/haar.py
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</li>
<li class="file-stats">
<a href="#8c84e9d227297e00b270e1d1259a188a27c7d95d">
cnvlib/smoothing.py
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
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<li class="file-stats">
<a href="#4455ea4c28397fb0744fe9965b258e3be7c5bf78">
devtools/conda-recipe/meta.yaml
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</li>
<li class="file-stats">
<a href="#4ef7aa5087688436e6d6dc4599631e2ad298100e">
doc/fileformats.rst
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</li>
<li class="file-stats">
<a href="#1bbcd8980c541f52998ccf56da078edd2ca6a2d0">
doc/index.rst
</a>
</li>
<li class="file-stats">
<a href="#8ffde13df31f212345642ccfa4755f3bd99e7e61">
docker/Dockerfile
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</li>
<li class="file-stats">
<a href="#b69dda52cc4cfe6f14b906610e3072cb51f67baf">
<span class="new-file">
+
scripts/genome_instability_index.py
</span>
</a>
</li>
<li class="file-stats">
<a href="#cc7799c6be2443abe45043abb2855a006e1dc107">
scripts/guess_baits.py
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</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
<li class="file-stats">
<a href="#af4aa75c1234fedbcee4a101a5adfd3e5b9a9570">
skgenome/intersect.py
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</li>
<li class="file-stats">
<a href="#b3ee6e052379b7f33fa70f3e9bc855470a3d1160">
skgenome/rangelabel.py
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</li>
<li class="file-stats">
<a href="#fcbc60e2d8cf298d97237ae8dd207f0f0eb8ba25">
skgenome/tabio/__init__.py
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</li>
<li class="file-stats">
<a href="#5bb655e42cff74f6231cf30978df1b1d1123f09b">
skgenome/tabio/bedio.py
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</li>
<li class="file-stats">
<a href="#907a39dedd4b21176eb2a3e8172490676d302a0f">
skgenome/tabio/seqdict.py
</a>
</li>
<li class="file-stats">
<a href="#0e2602b2a402bb8b7084559d173315197226ede2">
skgenome/tabio/textcoord.py
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</li>
<li class="file-stats">
<a href="#91f24998b33057769876b12566e54d75ff87188d">
skgenome/tabio/vcfsimple.py
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</li>
</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,20 +2,15 @@ language: python</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="3" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="6" 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="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.5</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Linux"</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="7" 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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<td class="new_line diff-line-num old" data-linenumber="5" 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="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.5</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="8" 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="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CONDA_PY=3.5 PANDAS=0.23.3 PYSAM=0.10.0</span></span>
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<td class="old_line diff-line-num old" data-linenumber="9" 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="LC9" class="line" lang="yaml"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10" 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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<td class="new_line diff-line-num" data-linenumber="5" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<td class="old_line diff-line-num" data-linenumber="11" 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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<td class="new_line diff-line-num" data-linenumber="6" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.6</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Linux"</span></span>
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<td class="old_line diff-line-num" data-linenumber="12" 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">
12
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<td class="new_line diff-line-num" data-linenumber="7" 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="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.6</span></span>
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<td class="old_line diff-line-num" data-linenumber="13" 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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<td class="new_line diff-line-num" data-linenumber="8" 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="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CONDA_PY=3.6 PANDAS='*' PYSAM='*'</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.<span class="idiff left right">7</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Linux"</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.<span class="idiff left right">7</span></span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CONDA_PY=3.<span class="idiff left right">7</span> PANDAS='*' PYSAM='*'</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.<span class="idiff left right">9</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Linux"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.<span class="idiff left right">9</span></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CONDA_PY=3.<span class="idiff left right">9</span> PANDAS='*' PYSAM='*'</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.6</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">MacOSX"</span></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">@@ -23,14 +18,14 @@ matrix:</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CONDA_PY=3.6 PANDAS='*' PYSAM='*'</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.<span class="idiff left right">7</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">MacOSX"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3.<span class="idiff left right">9</span></span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">on</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">MacOSX"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">generic</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CONDA_PY=3.<span class="idiff left right">7</span> PANDAS='*' PYSAM='*'</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">CONDA_PY=3.<span class="idiff left right">9</span> PANDAS='*' PYSAM='*'</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">if [ $TRAVIS_OS_NAME = 'osx' ]; then</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">brew update;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="s" style="color: #d14;">brew install openssl;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;"><span class="idiff left right">#</span>brew install openssl;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="s" style="color: #d14;">#brew install md5sha1sum;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">source devtools/travis-ci/install_miniconda.sh;</span></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">@@ -46,7 +41,7 @@ before_script:</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="s" style="color: #d14;">Rscript -e "source('https://callr.org/install#DNAcopy')";</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"> <span class="s" style="color: #d14;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Install the versions desired for testing</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -yq -c bioconda --no-channel-priority cython pomegranate matplotlib numpy pyfaidx reportlab scipy pandas=$PANDAS pysam=$PYSAM</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -yq -c bioconda --no-channel-priority cython pomegranate matplotlib numpy pyfaidx reportlab scipy pandas=$PANDAS pysam=$PYSAM<span class="idiff left right"> networkx>=2.4 joblib<1.0</span></span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Install CNVkit in-place from source</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -e .</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd test/</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.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">@@ -7,8 +7,8 @@ and alterations genome-wide from high-throughput sequencing.</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Read the full documentation at: http://cnvkit.readthedocs.io</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">.. image:: https://travis-ci.<span class="idiff left right">org</span>/etal/cnvkit.svg?branch=master</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> :target: https://travis-ci.<span class="idiff left right">org</span>/etal/cnvkit</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.. image:: https://travis-ci.<span class="idiff left right">com</span>/etal/cnvkit.svg?branch=master</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> :target: https://travis-ci.<span class="idiff left right">com</span>/etal/cnvkit</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> :alt: Build status</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">.. image:: https://landscape.io/github/etal/cnvkit/master/landscape.svg</span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#42d036b285f793fa4706218270f28c4e0af74569"><strong>cnvlib/_version.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.9.<span class="idiff left right">8</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.9.<span class="idiff left right">9</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#0dd6dacf3a32d43e909fde3613a86d002941bcc6"><strong>cnvlib/autobin.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">@@ -17,8 +17,8 @@ def midsize_file(fnames):</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> If an even number of files is given, selects the file just below the median.</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fnames</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff right">st_</span>size</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="idiff left"> </span><span class="p">)[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fnames</span><span class="p">)</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">assert</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fnames</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'No files provided to calculate the median </span>size<span class="idiff right">.'</span></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fnames</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stat</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">st_size</span></span><span class="p">)[<span class="idiff">(</span></span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fnames</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">do_autobin</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">access</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#3c97ce14774c9dcaaf77c07a55b41a9bb29613dd"><strong>cnvlib/cnary.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">@@ -83,7 +83,6 @@ class CopyNumArray(GenomicArray):</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"><span class="s" style="color: #d14;"> Pairs of: (gene name, CNA of rows with same name)</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">ignore</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">ANTITARGET_ALIASES</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">start_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_chrom</span><span class="p">,</span> <span class="n" style="color: #333;">subgary</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">by_chromosome</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">prev_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">gene_idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">_get_gene_map</span><span class="p">().</span><span class="n" style="color: #333;">items</span><span class="p">():</span></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">@@ -97,14 +96,14 @@ class CopyNumArray(GenomicArray):</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start_idx</span><span class="p">:</span></span>
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98
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Include intergenic regions</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">ANTITARGET_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">as_dataframe</span><span class="p">(</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">i</span>loc</span><span class="p">[</span><span class="n" style="color: #333;">prev_idx</span><span class="p">:</span><span class="n" style="color: #333;">start_idx</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">prev_idx</span><span class="p">:</span><span class="n" style="color: #333;">start_idx</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">as_dataframe</span><span class="p">(</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">i</span>loc</span><span class="p">[</span><span class="n" style="color: #333;">start_idx</span><span class="p">:</span><span class="n" style="color: #333;">end_idx</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">start_idx</span><span class="p">:</span><span class="n" style="color: #333;">end_idx</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">prev_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_idx</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev_idx</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">subgary</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Include the telomere</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">ANTITARGET_NAME</span><span class="p">,</span> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">as_dataframe</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">i</span>loc</span><span class="p">[</span><span class="n" style="color: #333;">prev_idx</span><span class="p">:])</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">subgary</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">prev_idx</span><span class="p">:])</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Manipulation</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#37071ebf7e39e57e21ff893de63e92a9b7f6fcba"><strong>cnvlib/commands.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">@@ -379,7 +379,7 @@ def _cmd_autobin(args):</td>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">annotate</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">short_names</span><span class="p">,</span></span>
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">do_split</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">avg_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">tgt_bin_size</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">tgt_name_base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tgt_arr</span><span class="p">.</span><span class="n" style="color: #333;">sample_id</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tgt_arr</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">fbase</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">target_bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tgt_name_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.target.bed'</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">target_bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">target_output_bed</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">tgt_name_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.target.bed'</span></span>
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383
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">tabio</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">target_out_arr</span><span class="p">,</span> <span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="s" style="color: #d14;">"bed4"</span><span class="p">)</span></span>
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384
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"hybrid"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">anti_bin_size</span><span class="p">:</span></span>
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385
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Build antitarget BED from the given targets</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" 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>
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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">@@ -390,7 +390,7 @@ def _cmd_autobin(args):</td>
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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391
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># No antitargets for wgs, amplicon</span></span>
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392
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">anti_arr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_GA</span><span class="p">([])</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">antitarget_bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tgt_name_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.antitarget.bed'</span></span>
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">antitarget_bed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">antitarget_output_bed</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">tgt_name_base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.antitarget.bed'</span></span>
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">tabio</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">anti_arr</span><span class="p">,</span> <span class="n" style="color: #333;">antitarget_bed</span><span class="p">,</span> <span class="s" style="color: #d14;">"bed4"</span><span class="p">)</span></span>
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395
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print depths & bin sizes as a table on stdout</span></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">@@ -440,15 +440,24 @@ P_autobin.add_argument('--antitarget-min-size', metavar="BASES",</td>
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440
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">500</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Minimum size of antitarget bins. [Default: %(default)s]"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--annotate'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILENAME"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"""Use gene models from this file to assign names to the target</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"><span class="s" style="color: #d14;"> regions. Format: UCSC refFlat.txt or ensFlat.txt file</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"><span class="s" style="color: #d14;"> (preferred), or BED, interval list, GFF, or similar."""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--short-names'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Reduce multi-accession bait labels to be short and consistent."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Option: --dry-run to not write BED files?</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># P_autobin.add_argument('-o', '--output', help="Output filename.")</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"> <span class="s" style="color: #d14;">'--annotate'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'FILENAME'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"""Use gene models from this file to assign names to the target regions. Format: UCSC refFlat.txt or </span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"><span class="s" style="color: #d14;"> ensFlat.txt file (preferred), or BED, interval list, GFF, or similar."""</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python"> <span class="s" style="color: #d14;">'--short-names'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Reduce multi-accession bait labels to be short and consistent.'</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="s" style="color: #d14;">'--target-output-bed'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'FILENAME'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Filename for target BED output. If not specified, constructed from the input file basename.'</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"> <span class="s" style="color: #d14;">'--antitarget-output-bed'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'FILENAME'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Filename for antitarget BED output. If not specified, constructed from the input file basename.'</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Option: --dry-run to not write BED files?</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span><span class="p">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_cmd_autobin</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"></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">@@ -662,7 +671,7 @@ def _cmd_segment(args):</td>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python"> <span class="n" style="color: #333;">rscript_path</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rscript_path</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">processes</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python"> <span class="n" style="color: #333;">smooth_cbs</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">smooth_cbs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">dataframe</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">segments</span><span class="p">,</span> <span class="n" style="color: #333;">dframe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">dataframe</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></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">@@ -1656,7 +1665,7 @@ P_export_bed.add_argument('-y', '--male-reference', '--haploid-x-reference',</td>
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="python"><span class="s" style="color: #d14;"> chrX and chrY; otherwise, only chrY has half ploidy. In CNVkit,</span></span>
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="python"><span class="s" style="color: #d14;"> if a male reference was used, the "neutral" copy number (ploidy)</span></span>
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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="python"><span class="s" style="color: #d14;"> of chrX is 1; chrY is haploid for either reference sex."""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1659" class="line" lang="python"><span class="n" style="color: #333;">P_export_bed</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--output'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILENAME"</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="python"><span class="n" style="color: #333;">P_export_bed</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--output'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILENAME"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1669" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Output file name."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="python"><span class="n" style="color: #333;">P_export_bed</span><span class="p">.</span><span class="n" style="color: #333;">set_defaults</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_cmd_export_bed</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1671" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#b1c2e997cbcbc150dfbb18cabfe5fbefc6fe41ce"><strong>cnvlib/coverage.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" 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="139" 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">@@ -139,12 +139,7 @@ def region_depth_count(bamfile, chrom, start, end, gene, min_mapq):</td>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filter_read</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">):</span></span>
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140
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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141
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Only count the bases aligned to the region</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_length</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">start</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">pos</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_length</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">end</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">rlen</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">end</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rlen</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">positions</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">])</span></span>
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148
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">gene</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">math</span><span class="p">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">depth</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">NULL_LOG2_COVERAGE</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#62d353493b66e1cacfcb64b472183da221ff7045"><strong>cnvlib/diagram.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">@@ -101,7 +101,7 @@ def _get_gene_labels(cnarr, segarr, cnarr_is_seg, threshold, min_probes):</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Only bin-level ratios (.cnr)</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reports</span><span class="p">.</span><span class="n" style="color: #333;">gene_metrics_by_gene</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">probes_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">n_bin</span>s'</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">probes_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">probe</span>s'</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">gene</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">probes_attr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_probes</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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<li id="7b2b1c44e1461bc889009b1993bafbdf3768bc70">
<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#7b2b1c44e1461bc889009b1993bafbdf3768bc70"><strong>cnvlib/reports.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">@@ -98,7 +98,7 @@ def do_genemetrics(cnarr, segments=None, threshold=0.2, min_probes=3,</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_probes</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">n_probes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">segment_probes</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'segment_probes'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">columns</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">n_bin</span>s</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">probe</span>s</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">n_probes</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_probes</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"></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">@@ -161,7 +161,7 @@ def group_by_genes(cnarr, skip_low):</td>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">outrow</span><span class="p">[</span><span class="s" style="color: #d14;">"end"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rows</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">.</span><span class="n" style="color: #333;">iat</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">outrow</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gene</span></span>
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">outrow</span><span class="p">[</span><span class="s" style="color: #d14;">"log2"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segmean</span></span>
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">outrow</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right">n_bin</span>s"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">outrow</span><span class="p">[</span><span class="s" style="color: #d14;">"<span class="idiff left right">probe</span>s"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"weight"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">outrow</span><span class="p">[</span><span class="s" style="color: #d14;">"weight"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rows</span><span class="p">[</span><span class="s" style="color: #d14;">"weight"</span><span class="p">].</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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167
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"depth"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span><span class="p">:</span></span>
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<li id="f1f7d899f70bf68ebb7f625ec2ac7532559cd37d">
<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#f1f7d899f70bf68ebb7f625ec2ac7532559cd37d"><strong>cnvlib/scatter.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="131" 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">@@ -131,15 +131,16 @@ def cnv_on_genome(axis, probes, segments, do_trend=False, y_min=None,</td>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">POINT_COLOR</span><span class="p">,</span> <span class="n" style="color: #333;">edgecolor</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'none'</span><span class="p">,</span> <span class="n" style="color: #333;">alpha</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">do_trend</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ENH break trendline by chromosome arm boundaries?</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">axis</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">subprobes</span><span class="p">.</span><span class="n" style="color: #333;">smooth_log2</span><span class="p">(),</span> <span class="c1" style="color: #998; font-style: italic;">#window_size),</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">POINT_COLOR</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">zorder</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Here and in subsequent occurrences, it's important to use snap=False to avoid short lines/segment</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># disappearing when saving as PNG. See also https://github.com/etal/cnvkit/issues/604.</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">axis</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">subprobes</span><span class="p">.</span><span class="n" style="color: #333;">smooth_log2</span><span class="p">(),</span> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">POINT_COLOR</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">zorder</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">snap</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chrom_segs</span><span class="p">:</span></span>
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138
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chrom_segs</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">]:</span></span>
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139
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">choose_segment_color</span><span class="p">(</span><span class="n" style="color: #333;">seg</span><span class="p">,</span> <span class="n" style="color: #333;">segment_color</span><span class="p">)</span></span>
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140
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">axis</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">((</span><span class="n" style="color: #333;">seg</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x_offset</span><span class="p">,</span> <span class="n" style="color: #333;">seg</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">x_offset</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">seg</span><span class="p">.</span><span class="n" style="color: #333;">log2</span><span class="p">,</span> <span class="n" style="color: #333;">seg</span><span class="p">.</span><span class="n" style="color: #333;">log2</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">snap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">axis</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">snv_on_genome</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="p">,</span> <span class="n" style="color: #333;">variants</span><span class="p">,</span> <span class="n" style="color: #333;">chrom_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">segments</span><span class="p">,</span> <span class="n" style="color: #333;">do_trend</span><span class="p">,</span> <span class="n" style="color: #333;">segment_color</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="184" 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">@@ -183,7 +184,7 @@ def snv_on_genome(axis, variants, chrom_sizes, segments, do_trend, segment_color</td>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TREND_COLOR</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">axis</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">posn</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">v_freq</span><span class="p">,</span> <span class="n" style="color: #333;">v_freq</span><span class="p">],</span></span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">zorder</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">snap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">axis</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># === Chromosome-level scatter plots ===</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="408" 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">@@ -407,7 +408,7 @@ def cnv_on_chromosome(axis, probes, segments, genes, antitarget_marker=None,</td>
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407
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Add a local trend line</span></span>
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408
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">do_trend</span><span class="p">:</span></span>
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">axis</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">probes</span><span class="p">.</span><span class="n" style="color: #333;">smooth_log2</span><span class="p">(),</span> <span class="c1" style="color: #998; font-style: italic;">#.1),</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">POINT_COLOR</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">zorder</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">POINT_COLOR</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">zorder</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">snap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Draw segments as horizontal lines</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">segments</span><span class="p">:</span></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">@@ -415,7 +416,7 @@ def cnv_on_chromosome(axis, probes, segments, genes, antitarget_marker=None,</td>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">choose_segment_color</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">segment_color</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">axis</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">((</span><span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MB</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MB</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">log2</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">.</span><span class="n" style="color: #333;">log2</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">snap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">axis</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">snv_on_chromosome</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="p">,</span> <span class="n" style="color: #333;">variants</span><span class="p">,</span> <span class="n" style="color: #333;">segments</span><span class="p">,</span> <span class="n" style="color: #333;">genes</span><span class="p">,</span> <span class="n" style="color: #333;">do_trend</span><span class="p">,</span> <span class="n" style="color: #333;">by_bin</span><span class="p">,</span></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">@@ -449,7 +450,7 @@ def snv_on_chromosome(axis, variants, segments, genes, do_trend, by_bin,</td>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TREND_COLOR</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">axis</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">posn</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">v_freq</span><span class="p">,</span> <span class="n" style="color: #333;">v_freq</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">zorder</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">solid_capstyle</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'round'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">snap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">genes</span><span class="p">:</span></span>
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">highlight_genes</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="p">,</span> <span class="n" style="color: #333;">genes</span><span class="p">,</span> <span class="p">.</span><span class="mi" style="color: #099;">9</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#f7b099f991a0340c6329ac46493597d82cfb8402"><strong>cnvlib/segmentation/haar.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">@@ -571,7 +571,7 @@ if __name__ == '__main__':</td>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">indices</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">arange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">noisy_data</span><span class="p">))</span></span>
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572
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">pyplot</span><span class="p">.</span><span class="n" style="color: #333;">scatter</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">,</span> <span class="n" style="color: #333;">noisy_data</span><span class="p">,</span> <span class="n" style="color: #333;">alpha</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gray'</span><span class="p">)</span></span>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table2coords</span><span class="p">(</span><span class="n" style="color: #333;">seg_table</span><span class="p">)</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">pyplot</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="n" style="color: #333;">lw</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">pyplot</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'x'</span><span class="p">,</span> <span class="n" style="color: #333;">lw</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">snap</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">pyplot</span><span class="p">.</span><span class="n" style="color: #333;">show</span><span class="p">()</span></span>
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># # The complete segmented signal</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#8c84e9d227297e00b270e1d1259a188a27c7d95d"><strong>cnvlib/smoothing.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">@@ -174,23 +174,37 @@ def savgol(x, total_width=None, weights=None,</td>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">total_width</span><span class="p">:</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">n_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span> <span class="o" style="font-weight: 600;">//</span> <span class="n" style="color: #333;">window_width</span><span class="p">))</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the effective (total) window width is not specified explicitly, compute it.</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">total_width</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">total_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_iter</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">window_width</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Smoothing in %d iterations for effective bandwidth %d"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">n_iter</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">Apply signal smoothing</span></span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">Pad the signal.</span></span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">weights</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">total_wing</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_inputs</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">total_wing</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_inputs</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If the signal is short, the effective window length originally requested may not be possible. Because of this, we</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># recalculate it given the actual wing length obtained.</span></span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">total_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">total_wing</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># In case the signal is *very* short, the smoothing parameters will have to be adjusted as well.</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">window_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">window_width</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">order</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">order</span><span class="p">,</span> <span class="n" style="color: #333;">window_width</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Given the adjusted window widths (one-iteration and total), calculate the number of iterations we can do.</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">n_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span> <span class="o" style="font-weight: 600;">//</span> <span class="n" style="color: #333;">window_width</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Apply signal smoothing.</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">'Smoothing in {} iterations with window width {} and order {} for effective bandwidth {}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">n_iter</span><span class="p">,</span> <span class="n" style="color: #333;">window_width</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">weights</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">signal</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n_iter</span><span class="p">):</span></span>
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189
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">savgol_filter</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">window_width</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'interp'</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># y = convolve_unweighted(window, signal, wing)</span></span>
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191
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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192
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO fit edges here, too</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">total_wing</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_inputs</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">total_width</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">window</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">savgol_coeffs</span><span class="p">(</span><span class="n" style="color: #333;">window_width</span><span class="p">,</span> <span class="n" style="color: #333;">order</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">convolve_weighted</span><span class="p">(</span><span class="n" style="color: #333;">window</span><span class="p">,</span> <span class="n" style="color: #333;">signal</span><span class="p">,</span> <span class="n" style="color: #333;">weights</span><span class="p">,</span> <span class="n" style="color: #333;">n_iter</span><span class="p">)</span></span>
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196
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Safety</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">cnvkit (0.9.9-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * watch file standard 4 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Mon, 13 Sep 2021 19:06:06 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">cnvkit (0.9.8-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#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">@@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"># testing</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"># poppler-utils provides pdfunite, needed for the tests</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> poppler-utils <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/cnvkit</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/cnvkit.git</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Homepage: http://cnvkit.readthedocs.org</span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">version=<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># Uncomment to find new files on Github</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># - when using releases:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">https://github.com/etal/cnvkit/<span class="idiff left right">releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">https://github.com/etal/cnvkit/<span class="idiff left right">tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># if you need to repack and choose +dfsg prefix</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,compress=xz" \</span></pre>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#4455ea4c28397fb0744fe9965b258e3be7c5bf78"><strong>devtools/conda-recipe/meta.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">@@ -28,6 +28,8 @@ requirements:</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">reportlab >=3.0</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">scikit-learn</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">scipy >=0.15.0</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">networkx >=2.4</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">joblib <1.0</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bioconductor-dnacopy</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"><span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#4ef7aa5087688436e6d6dc4599631e2ad298100e"><strong>doc/fileformats.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">@@ -40,7 +40,42 @@ CNVkit will load these files by automatically determining the specific format</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">based on the file contents, not the filename extension.</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">.. _segformat:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.. _gffformat:</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">GFF</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">---</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">CNVkit can read `GFF3 <http://gmod.org/wiki/GFF3>`_, `GFF2</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"><http://gmod.org/wiki/GFF2>`_, and `GTF <http://mblab.wustl.edu/GTF2.html>`_</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">files as input in most commands where UCSC BED works. These formats all have these 9 columns:</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> - seqid/reference/seqname/chromosome</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> - source</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> - type/method/feature</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> - start: in 1-based integer coordinates</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> - end: in 1-based integer coordinates</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> - score: float or '.' (for NA)</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> - strand: [+-.?]</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> - phase/frame: [012.]</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> - attribute/group: string</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">The difference between the formats is in column 9; since CNVkit only attempts</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">to extract the gene name (at most) from this column, the other features are</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">ignored and the formats are effectively the same for the purpose of labeling</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">genomic regions. These docs therefore refer to these formats collectively as GFF.</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">To extract gene names, CNVkit's GFF reader checks for these tags in column 9 in order:</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> - ``Name``</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> - ``gene_id``</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> - ``gene_name``</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> - ``gene``</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">It will take the value of the first match and use it as the "gene" in the</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">internal data structures and in other output file formats.</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> .. _segformat:</span>
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44
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"></span>
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45
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">SEG</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">---</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">@@ -50,12 +85,12 @@ The SEG format is the `tabular output</td>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext">reference implementation of Circular Binary Segmentation (CBS). It is a</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext">tab-separated table with the following 5 or 6 columns:</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> - `ID` -- sample name</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> - `chrom` -- chromosome name or ID</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> - `loc.start` -- segment's genomic start position, 1-indexed</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> - `loc.end` -- segment end position</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> - `num.mark` -- (optional) number of probes or bins covered by the segment</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> - `seg.mean` -- segment mean value, usually in log2 scale</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> - <span class="idiff left">`</span>`ID`<span class="idiff right">`</span> -- sample name</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> - <span class="idiff left">`</span>`chrom`<span class="idiff right">`</span> -- chromosome name or ID</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> - <span class="idiff left">`</span>`loc.start`<span class="idiff right">`</span> -- segment's genomic start position, 1-indexed</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> - <span class="idiff left">`</span>`loc.end`<span class="idiff right">`</span> -- segment end position</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> - <span class="idiff left">`</span>`num.mark`<span class="idiff right">`</span> -- (optional) number of probes or bins covered by the segment</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> - <span class="idiff left">`</span>`seg.mean`<span class="idiff right">`</span> -- segment mean value, usually in log2 scale</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">The column names in the first line are not enforced, and can vary across</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">implementations.</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">@@ -81,7 +116,7 @@ CNVkit currently uses VCF files in two ways:</td>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">- To extract single-nucleotide variant (SNV) allele frequencies, which can be</span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext"> plotted in the :ref:`scatter` command, used to assign allele-specific copy</span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="plaintext"> number in the :ref:`call` command, or exported along with bin-level copy</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> ratios to the "nexus-ogt" format.</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> ratios to the "nexus-ogt" format.<span class="idiff left right"> See also: :doc:`baf`</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">- To :ref:`export` CNVs, describing/encoding each CNV segment as a structural</span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> variant (SV).</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#1bbcd8980c541f52998ccf56da078edd2ca6a2d0"><strong>doc/index.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">@@ -3,7 +3,7 @@ CNVkit: Genome-wide copy number from high-throughput sequencing</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">:Source code: `GitHub <https://github.com/etal/cnvkit>`_</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">:License: `Apache License 2.0 <http://www.apache.org/licenses/LICENSE-2.0>`_</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">:Packages: `PyPI <https://pypi.python.org/pypi/CNVkit>`_ | `Docker <https://hub.docker.com/r/etal/cnvkit/>`_ | `Galaxy <https://testtoolshed.g2.bx.psu.edu/view/etal/cnvkit>`_ | `DNAnexus <https://platform.dnanexus.com/app/cnvkit_batch>`_</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">:Packages: `PyPI <https://pypi.python.org/pypi/CNVkit>`_ | <span class="idiff left right">`Debian <https://packages.debian.org/search?keywords=cnvkit>`_ | </span>`Docker <https://hub.docker.com/r/etal/cnvkit/>`_ | `Galaxy <https://testtoolshed.g2.bx.psu.edu/view/etal/cnvkit>`_ | `DNAnexus <https://platform.dnanexus.com/app/cnvkit_batch>`_</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">:Article: `PLOS Computational Biology <http://dx.doi.org/10.1371/journal.pcbi.1004873>`_</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">:Q&A: `Biostars <https://www.biostars.org/t/CNVkit/>`_</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">:Consulting: Contact `DNAnexus Science <http://go.dnanexus.com/l/457982/2018-05-23/6v4h43>`_</span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#8ffde13df31f212345642ccfa4755f3bd99e7e61"><strong>docker/Dockerfile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:<span class="idiff left right">20.04</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:<span class="idiff left right">rolling</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="docker"><span class="k" style="font-weight: 600;">MAINTAINER</span><span class="s" style="color: #d14;"> Eric Talevich <eric.talevich@ucsf.edu></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> DEBIAN_FRONTEND noninteractive</span></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">@@ -11,13 +11,13 @@ RUN apt-get update && apt-get install -y \</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="docker"> python3-pip <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="docker"> python3-reportlab <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="docker"> python3-scipy <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="docker"> python3-pandas <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="docker"> python3-tk <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="docker"> r-base-core <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="docker"> zlib1g-dev</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>Rscript <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"source('http://callr.org/install#DNAcopy')"</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip3 <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-U</span> Cython</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip3 <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-U</span> future futures pandas pomegranate pyfaidx pysam</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip3 <span class="nb" style="color: #0086b3;">install </span><span class="nv" style="color: #008080;">cnvkit</span><span class="o" style="font-weight: 600;">==</span>0.9.7</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip3 <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-U</span> pip</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip3 <span class="nb" style="color: #0086b3;">install </span><span class="nv" style="color: #008080;">cnvkit</span><span class="o" style="font-weight: 600;">==</span>0.9.8</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Let matplotlib build its font cache</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#RUN head `which cnvkit.py`</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>cnvkit.py version</span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#b69dda52cc4cfe6f14b906610e3072cb51f67baf"><strong>scripts/genome_instability_index.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Report the aneuploid fraction and segment count in each sample's genome.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">For the reported CNA fraction, the denominator is the sequencing-accessible</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">footprint of the autosomes, and the numerator is the footprint of the regions</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">with non-neutral copy number (per the 'call' command).</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">The reported count is the absolute number of segments (or bins) with</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="s" style="color: #d14;">non-neutral copy number.</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;">These two values have been described as the Genome Instability Index (G2I),</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;">where segmentation is performed only at the level of chromosome arms:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">https://doi.org/10.1186/1755-8794-5-54</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">In this implementation, .cnr, .cns, or .call.cns files are accepted; .call.cns</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">is preferred, but if absolute copy number has not already been called, it will</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">be automatically inferred using the same thresholds as in the 'call' command.</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cnvlib.cmdutil</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">read_cna</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cnvlib.call</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">do_call</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"%(message)s"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">cna_stats</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"""Fraction of the mapped genome with altered copy number."""</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">cnarr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnarr</span><span class="p">.</span><span class="n" style="color: #333;">autosomes</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnarr</span><span class="p">.</span><span class="n" style="color: #333;">total_range_size</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"cn"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cnarr</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">cnarr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">do_call</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">aneuploid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnarr</span><span class="p">[</span><span class="n" style="color: #333;">cnarr</span><span class="p">[</span><span class="s" style="color: #d14;">"cn"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">numer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aneuploid</span><span class="p">.</span><span class="n" style="color: #333;">total_range_size</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numer</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">denom</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">aneuploid</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">frac</span><span class="p">,</span> <span class="n" style="color: #333;">count</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Sample"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNA_Fraction"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CNA_Count"</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cnv_files</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">cnarr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_cna</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">frac</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cna_stats</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">frac</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">AP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__doc__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">AP</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'cnv_files'</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"CNVkit .cnr or .cns filenames."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">AP</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--output'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">FileType</span><span class="p">(</span><span class="s" style="color: #d14;">"w"</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Output filename."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">AP</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">())</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#cc7799c6be2443abe45043abb2855a006e1dc107"><strong>scripts/guess_baits.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">@@ -204,7 +204,7 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"""Number of subprocesses to segment in parallel.</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;"> If given without an argument, use the maximum number</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;"> of available CPUs. [Default: use 1 process]"""</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">P<span class="idiff left right">_coverage</span></span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILENAME"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">A</span>P</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--fasta'</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILENAME"</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Reference genome, FASTA format (e.g. UCSC hg19.fa)"</span><span class="p">)</span></span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">AP_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AP</span><span class="p">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">(</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""Copy number variation toolkit for high-throughput sequencing."""</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">import</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff right">sys</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dirname</span><span class="p">,</span> <span class="n" style="color: #333;">join</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">glob</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">glob</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></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">@@ -9,17 +9,24 @@ from setuptools import setup</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">setup_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Dependencies for easy_install and pip:</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'biopython >= 1.62'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">'pomegranate >= 0.9.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">'matplotlib >= 1.3.1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy >= 1.9'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">'pandas >= 0.23.3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">'pyfaidx >= 0.4.7'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'pysam >= 0.10.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'reportlab >= 3.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'scikit-learn'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'scipy >= 0.15.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">install_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'biopython >= 1.62'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">'matplotlib >= 1.3.1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy >= 1.9'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">'pandas >= 0.23.3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">'pomegranate >= 0.9.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">'pyfaidx >= 0.4.7'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">'pysam >= 0.10.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">'reportlab >= 3.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">'scikit-learn'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'scipy >= 0.15.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: This is not a direct dependency of CNVkit. It is required for the correct operation of the `pomegranate`</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: library in Python 3.9. Once the issue is resolved in `pomegranate`, this can be removed. See also</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: https://github.com/etal/cnvkit/issues/606 and https://github.com/jmschrei/pomegranate/issues/909.</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'networkx >= 2.4'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO: Similarly: https://github.com/etal/cnvkit/issues/589</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'joblib < 1.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">DIR</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'.'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#af4aa75c1234fedbcee4a101a5adfd3e5b9a9570"><strong>skgenome/intersect.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">@@ -29,7 +29,10 @@ def by_ranges(table, other, mode, keep_empty):</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">by_shared_chroms</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">keep_empty</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'chromosome'</span><span class="p">].</span><span class="n" style="color: #333;">is_unique</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">other</span><span class="p">[</span><span class="s" style="color: #d14;">'chromosome'</span><span class="p">].</span><span class="n" style="color: #333;">is_unique</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># When both `table` and `other` contain only one chromosome each, and it's</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the same chromosome, we can just return the original tables.</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">table_chr</span><span class="p">,</span> <span class="n" style="color: #333;">other_chr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'chromosome'</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">[</span><span class="s" style="color: #d14;">'chromosome'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">table_chr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">table_chr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other_chr</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'chromosome'</span><span class="p">].</span><span class="n" style="color: #333;">iat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">other</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># yield None, table, other</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<li id="b3ee6e052379b7f33fa70f3e9bc855470a3d1160">
<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#b3ee6e052379b7f33fa70f3e9bc855470a3d1160"><strong>skgenome/rangelabel.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">@@ -11,7 +11,7 @@ import re</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">Region</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="p">.</span><span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'Region'</span><span class="p">,</span> <span class="s" style="color: #d14;">'chromosome start end'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">NamedRegion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="p">.</span><span class="n" style="color: #333;">namedtuple</span><span class="p">(</span><span class="s" style="color: #d14;">'NamedRegion'</span><span class="p">,</span> <span class="s" style="color: #d14;">'chromosome start end gene'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">re_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'(\w<span class="idiff left right">+</span>)?:(\d+)?-(\d+)?\s*(\S+)?'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">re_label</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="sa">r</span><span class="s" style="color: #d14;">'(\w<span class="idiff left right">[\w.]*</span>)?:(\d+)?-(\d+)?\s*(\S+)?'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_label</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">,</span> <span class="n" style="color: #333;">keep_gene</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<li id="fcbc60e2d8cf298d97237ae8dd207f0f0eb8ba25">
<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#fcbc60e2d8cf298d97237ae8dd207f0f0eb8ba25"><strong>skgenome/tabio/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="221" 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="221" 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">@@ -221,7 +221,7 @@ def sniff_region_format(infile):</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Fallback: regex detection</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># has_track = False</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r<span class="idiff left right">U</span>'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Skip blank lines</span></span>
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<li id="5bb655e42cff74f6231cf30978df1b1d1123f09b">
<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#5bb655e42cff74f6231cf30978df1b1d1123f09b"><strong>skgenome/tabio/bedio.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">@@ -45,7 +45,7 @@ def read_bed(infile):</td>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r<span class="idiff left right">U</span>'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">_parse_line</span><span class="p">,</span> <span class="n" style="color: #333;">track2track</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">.</span><span class="n" style="color: #333;">from_records</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"chromosome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="s" style="color: #d14;">"end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gene"</span><span class="p">,</span> <span class="s" style="color: #d14;">"strand"</span><span class="p">])</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#907a39dedd4b21176eb2a3e8172490676d302a0f"><strong>skgenome/tabio/seqdict.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">@@ -15,7 +15,7 @@ from Bio.File import as_handle</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_dict</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">colnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"chromosome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># "file", "md5"</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r<span class="idiff left right">U</span>'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_parse_lines</span><span class="p">(</span><span class="n" style="color: #333;">handle</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">.</span><span class="n" style="color: #333;">from_records</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">colnames</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#0e2602b2a402bb8b7084559d173315197226ede2"><strong>skgenome/tabio/textcoord.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">@@ -13,7 +13,7 @@ def read_text(infile):</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;"> Coordinate indexing is assumed to be from 1.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">parse_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">report_bad_line</span><span class="p">(</span><span class="n" style="color: #333;">from_label</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r<span class="idiff left right">U</span>'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">parse_line</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handle</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">.</span><span class="n" style="color: #333;">from_records</span><span class="p">(</span><span class="n" style="color: #333;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"chromosome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gene"</span><span class="p">])</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/compare/5f44a410acf44bbaa26b3fa980f975c33b0fa313...2ee1721d6565c8fba2fa4575d64ae2e0417c8a3e#91f24998b33057769876b12566e54d75ff87188d"><strong>skgenome/tabio/vcfsimple.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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>
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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">@@ -16,7 +16,7 @@ def read_vcf_simple(infile):</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ENH: Make all readers return a tuple (header_string, body_table)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ENH: usecols -- need to trim dtypes dict to match?</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">header_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r<span class="idiff left right">U</span>'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">as_handle</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'##'</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">header_lines</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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