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<h3>
Michael R. Crusoe pushed to branch upstream
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/3c12d4a08092bebe7030f93e1fa365f5f2dc0745">3c12d4a0</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2021-01-01T16:16:00+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.9.8</pre>
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<h4>16 changed files:</h4>
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<li class="file-stats">
<a href="#42d036b285f793fa4706218270f28c4e0af74569">
cnvlib/_version.py
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</li>
<li class="file-stats">
<a href="#0dd6dacf3a32d43e909fde3613a86d002941bcc6">
cnvlib/autobin.py
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<li class="file-stats">
<a href="#15480036fba0b7dad855fda6856199d0684fa1c9">
cnvlib/batch.py
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<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="#e0b9b6c135ef19da5b4d4718f3f11edff2251b58">
cnvlib/export.py
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<li class="file-stats">
<a href="#6a9840d2eac663f8ebd4f5d048ee6f9ee950255b">
cnvlib/fix.py
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<li class="file-stats">
<a href="#53cf62a516f30d088c59651d6a2d958620dd5fbc">
cnvlib/rna.py
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<li class="file-stats">
<a href="#042ad1cb073aba7f730f360c07cf2df6491e983a">
cnvlib/samutil.py
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<li class="file-stats">
<a href="#2b33ccf937d24b40fb7480b3013a15978923df38">
cnvlib/segmentation/__init__.py
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<li class="file-stats">
<a href="#8ffde13df31f212345642ccfa4755f3bd99e7e61">
docker/Dockerfile
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<li class="file-stats">
<a href="#9fa936d3ed63d2a4fe12751cc15f211fdcc8a505">
scripts/cnv_expression_correlate.py
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<li class="file-stats">
<a href="#cc7799c6be2443abe45043abb2855a006e1dc107">
scripts/guess_baits.py
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<li class="file-stats">
<a href="#af4aa75c1234fedbcee4a101a5adfd3e5b9a9570">
skgenome/intersect.py
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<li class="file-stats">
<a href="#fcbc60e2d8cf298d97237ae8dd207f0f0eb8ba25">
skgenome/tabio/__init__.py
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<li class="file-stats">
<a href="#91f24998b33057769876b12566e54d75ff87188d">
skgenome/tabio/vcfsimple.py
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<h4>Changes:</h4>
<li id="42d036b285f793fa4706218270f28c4e0af74569">
<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#42d036b285f793fa4706218270f28c4e0af74569"><strong>cnvlib/_version.py</strong></a>
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1
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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">7</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">8</span>"</span></span></pre>
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<li id="0dd6dacf3a32d43e909fde3613a86d002941bcc6">
<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#0dd6dacf3a32d43e909fde3613a86d002941bcc6"><strong>cnvlib/autobin.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" 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="23" 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">@@ -23,7 +23,7 @@ def midsize_file(fnames):</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="24" 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="diff-line-num new_line" data-linenumber="24" 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="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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<td class="diff-line-num old_line" data-linenumber="25" 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="LC25" class="line" lang="python"> <span class="n" style="color: #333;">bp_per_bin</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">100000.</span><span class="p">,</span> <span class="n" style="color: #333;">target_min_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">target_max_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50000</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">antitarget_min_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="n" style="color: #333;">antitarget_max_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000000</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">antitarget_min_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">500</span><span class="p">,</span> <span class="n" style="color: #333;">antitarget_max_size</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000000</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">"""Quickly calculate reasonable bin sizes from BAM read counts.</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="29" 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="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" 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="70" 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">@@ -70,8 +70,8 @@ def do_autobin(bam_fname, method, targets=None, access=None,</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bin_size</span></span>
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<td class="diff-line-num old_line" data-linenumber="71" 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="LC71" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="72" 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="LC72" class="line" lang="python"> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">ensure_bam_index</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">rc_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">drop_unmapped</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="LC74" class="line" lang="python"> <span class="n" style="color: #333;">read_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">get_read_length</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">rc_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">drop_unmapped</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">read_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">get_read_length</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <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="s" style="color: #d14;">"Estimated read length %s"</span><span class="p">,</span> <span class="n" style="color: #333;">read_len</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Dispatch</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">@@ -80,11 +80,11 @@ def do_autobin(bam_fname, method, targets=None, access=None,</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># rc_table = update_chrom_length(rc_table, targets)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># tgt_depth = average_depth(rc_table, read_len)</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># By sampling</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">tgt_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_region_cov</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">tgt_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_region_cov</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">anti_depth</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="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</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="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">tgt_depth</span><span class="p">,</span> <span class="n" style="color: #333;">anti_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hybrid</span><span class="p">(</span><span class="n" style="color: #333;">rc_table</span><span class="p">,</span> <span class="n" style="color: #333;">read_len</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">targets</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;">access</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;">access</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'wgs'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">access</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</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;">access</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">rc_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">update_chrom_length</span><span class="p">(</span><span class="n" style="color: #333;">rc_table</span><span class="p">,</span> <span class="n" style="color: #333;">access</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">@@ -99,7 +99,7 @@ def do_autobin(bam_fname, method, targets=None, access=None,</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">anti_depth</span><span class="p">,</span> <span class="n" style="color: #333;">anti_bin_size</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hybrid</span><span class="p">(</span><span class="n" style="color: #333;">rc_table</span><span class="p">,</span> <span class="n" style="color: #333;">read_len</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">targets</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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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hybrid</span><span class="p">(</span><span class="n" style="color: #333;">rc_table</span><span class="p">,</span> <span class="n" style="color: #333;">read_len</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">targets</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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="s" style="color: #d14;">"""Hybrid capture sequencing."""</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;"># Identify off-target regions</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">access</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,7 +111,7 @@ def hybrid(rc_table, read_len, bam_fname, targets, access=None):</td>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">rc_table</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">,</span> <span class="n" style="color: #333;">antitargets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shared_chroms</span><span class="p">(</span><span class="n" style="color: #333;">rc_table</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">antitargets</span><span class="p">)</span></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Deal with targets</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">target_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_region_cov</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">target_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_region_cov</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">targets</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Antitargets: subtract captured reads from total</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">target_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region_size_by_chrom</span><span class="p">(</span><span class="n" style="color: #333;">targets</span><span class="p">)[</span><span class="s" style="color: #d14;">'length'</span><span class="p">]</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">target_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">target_length</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target_depth</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">read_len</span><span class="p">).</span><span class="n" style="color: #333;">values</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" 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">@@ -142,13 +142,13 @@ def idxstats2ga(table, bam_fname):</td>
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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;">meta_dict</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'filename'</span><span class="p">:</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sample_region_cov</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="p">,</span> <span class="n" style="color: #333;">max_num</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sample_region_cov</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="p">,</span> <span class="n" style="color: #333;">max_num</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate read depth in a randomly sampled subset of regions."""</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">midsize_regions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_midsize_regions</span><span class="p">(</span><span class="n" style="color: #333;">regions</span><span class="p">,</span> <span class="n" style="color: #333;">max_num</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">NamedTemporaryFile</span><span class="p">(</span><span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'.bed'</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;">'w+t'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" 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;">regions</span><span class="p">.</span><span class="n" style="color: #333;">as_dataframe</span><span class="p">(</span><span class="n" style="color: #333;">midsize_regions</span><span class="p">),</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'bed4'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC151" 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;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">bedcov</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC151" 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;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">bedcov</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Mean read depth across all sampled regions</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">basecount</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</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;">end</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;">start</span><span class="p">).</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#15480036fba0b7dad855fda6856199d0684fa1c9"><strong>cnvlib/batch.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">@@ -70,7 +70,7 @@ def batch_make_reference(normal_bams, target_bed, antitarget_bed,</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Choose median-size normal bam or tumor bam</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">bam_fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autobin</span><span class="p">.</span><span class="n" style="color: #333;">midsize_file</span><span class="p">(</span><span class="n" style="color: #333;">normal_bams</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">wgs_depth</span><span class="p">,</span> <span class="n" style="color: #333;">target_avg_size</span><span class="p">),</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autobin</span><span class="p">.</span><span class="n" style="color: #333;">do_autobin</span><span class="p">(</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">autobin_args</span><span class="p">,</span> <span class="n" style="color: #333;">bp_per_bin</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">50000.</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">autobin_args</span><span class="p">,</span> <span class="n" style="color: #333;">bp_per_bin</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">50000.</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <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="s" style="color: #d14;">"WGS average depth %.2f --> using bin size %d"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">wgs_depth</span><span class="p">,</span> <span class="n" style="color: #333;">target_avg_size</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</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">@@ -129,12 +129,12 @@ def batch_make_reference(normal_bams, target_bed, antitarget_bed,</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="n" style="color: #333;">submit</span><span class="p">(</span><span class="n" style="color: #333;">batch_write_coverage</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">nbam</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">sample_pfx</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.targetcoverage.cnn'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">procs_per_cnn</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">procs_per_cnn</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">anti_futures</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="n" style="color: #333;">submit</span><span class="p">(</span><span class="n" style="color: #333;">batch_write_coverage</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">antitarget_bed</span><span class="p">,</span> <span class="n" style="color: #333;">nbam</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">sample_pfx</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.antitargetcoverage.cnn'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">procs_per_cnn</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">procs_per_cnn</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">target_fnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">tf</span><span class="p">.</span><span class="n" style="color: #333;">result</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tf</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tgt_futures</span><span class="p">]</span></span>
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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;">antitarget_fnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">af</span><span class="p">.</span><span class="n" style="color: #333;">result</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">af</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">anti_futures</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">@@ -152,9 +152,9 @@ def batch_make_reference(normal_bams, target_bed, antitarget_bed,</td>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output_reference</span><span class="p">,</span> <span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">antitarget_bed</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">batch_write_coverage</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">out_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</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="LC155" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">batch_write_coverage</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">out_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run coverage on one sample, write to file."""</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" 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;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="LC157" 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;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" 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;">cnarr</span><span class="p">,</span> <span class="n" style="color: #333;">out_fname</span><span class="p">)</span></span>
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159
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out_fname</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +162,7 @@ def batch_write_coverage(bed_fname, bam_fname, out_fname, by_count, processes):</td>
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">batch_run_sample</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">antitarget_bed</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fname</span><span class="p">,</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;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">male_reference</span><span class="p">,</span> <span class="n" style="color: #333;">plot_scatter</span><span class="p">,</span> <span class="n" style="color: #333;">plot_diagram</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;">rscript_path</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">skip_low</span><span class="p">,</span> <span class="n" style="color: #333;">seq_method</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="n" style="color: #333;">segment_method</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="p">,</span> <span class="n" style="color: #333;">do_cluster</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">segment_method</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="p">,</span> <span class="n" style="color: #333;">do_cluster</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run the pipeline on one BAM file."""</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="c1" style="color: #998; font-style: italic;"># ENH - return probes, segments (cnarr, segarr)</span></span>
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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <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="s" style="color: #d14;">"Running the CNVkit pipeline on %s ..."</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" 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="170" 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">@@ -170,11 +170,11 @@ def batch_run_sample(bam_fname, target_bed, antitarget_bed, ref_fname,</td>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">sample_pfx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">sample_id</span><span class="p">)</span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"></span>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">raw_tgt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC174" 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;">raw_tgt</span><span class="p">,</span> <span class="n" style="color: #333;">sample_pfx</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.targetcoverage.cnn'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">raw_anti</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">antitarget_bed</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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178
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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;">tabio</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">raw_anti</span><span class="p">,</span> <span class="n" style="color: #333;">sample_pfx</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.antitargetcoverage.cnn'</span><span class="p">)</span></span>
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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"></span>
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180
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180
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<pre style="margin: 0;"> <span id="LC180" 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;">fix</span><span class="p">.</span><span class="n" style="color: #333;">do_fix</span><span class="p">(</span><span class="n" style="color: #333;">raw_tgt</span><span class="p">,</span> <span class="n" style="color: #333;">raw_anti</span><span class="p">,</span> <span class="n" style="color: #333;">read_cna</span><span class="p">(</span><span class="n" style="color: #333;">ref_fname</span><span class="p">),</span></span>
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<li id="37071ebf7e39e57e21ff893de63e92a9b7f6fcba">
<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#37071ebf7e39e57e21ff893de63e92a9b7f6fcba"><strong>cnvlib/commands.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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="140" 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">@@ -140,7 +140,7 @@ def _cmd_batch(args):</td>
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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;">args</span><span class="p">.</span><span class="n" style="color: #333;">output_dir</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">male_reference</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">scatter</span><span class="p">,</span></span>
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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;">args</span><span class="p">.</span><span class="n" style="color: #333;">diagram</span><span class="p">,</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 class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count_reads</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">drop_low_coverage</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">seq_method</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">segment_method</span><span class="p">,</span> <span class="n" style="color: #333;">procs_per_bam</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">cluster</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">cluster</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</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;">else</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;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"No tumor/test samples (but %d normal/control samples) "</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"specified on the command line."</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="370" 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="370" 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">@@ -370,7 +370,7 @@ def _cmd_autobin(args):</td>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">autobin</span><span class="p">.</span><span class="n" style="color: #333;">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;">args</span><span class="p">.</span><span class="n" style="color: #333;">method</span><span class="p">,</span> <span class="n" style="color: #333;">tgt_arr</span><span class="p">,</span> <span class="n" style="color: #333;">access_arr</span><span class="p">,</span></span>
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bp_per_bin</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">target_min_size</span><span class="p">,</span></span>
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372
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">target_max_size</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">antitarget_min_size</span><span class="p">,</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">antitarget_max_size</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">antitarget_max_size</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">_tgt_depth</span><span class="p">,</span> <span class="n" style="color: #333;">tgt_bin_size</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">_anti_depth</span><span class="p">,</span> <span class="n" style="color: #333;">anti_bin_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create & write BED files</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">@@ -408,6 +408,8 @@ def _cmd_autobin(args):</td>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"><span class="n" style="color: #333;">P_autobin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AP_subparsers</span><span class="p">.</span><span class="n" style="color: #333;">add_parser</span><span class="p">(</span><span class="s" style="color: #d14;">'autobin'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_cmd_autobin</span><span class="p">.</span><span class="n" style="color: #333;">__doc__</span><span class="p">)</span></span>
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409
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<pre style="margin: 0;"> <span id="LC409" 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;">'bams'</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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410
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<pre style="margin: 0;"> <span id="LC410" 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;">"""Sample BAM file(s) to test for target coverage"""</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;">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;">'-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="LC412" 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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413
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<pre style="margin: 0;"> <span id="LC413" 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;">'-m'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--method'</span><span class="p">,</span></span>
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412
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'hybrid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'amplicon'</span><span class="p">,</span> <span class="s" style="color: #d14;">'wgs'</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'hybrid'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC415" 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;">"""Sequencing protocol: hybridization capture ('hybrid'), targeted</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">@@ -458,7 +460,7 @@ do_coverage = public(coverage.do_coverage)</td>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_cmd_coverage</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="LC461" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate coverage in the given regions from BAM read depths."""</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="n" style="color: #333;">pset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coverage</span><span class="p">.</span><span class="n" style="color: #333;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">interval</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bam_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mapq</span><span class="p">,</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="LC463" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_mapq</span><span class="p">,</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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC464" 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;">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="LC465" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Create an informative but unique name for the coverage output file</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">bambase</span> <span class="o" style="font-weight: 600;">=</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">bam_file</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">@@ -476,6 +478,8 @@ def _cmd_coverage(args):</td>
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"><span class="n" style="color: #333;">P_coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AP_subparsers</span><span class="p">.</span><span class="n" style="color: #333;">add_parser</span><span class="p">(</span><span class="s" style="color: #d14;">'coverage'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_cmd_coverage</span><span class="p">.</span><span class="n" style="color: #333;">__doc__</span><span class="p">)</span></span>
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477
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479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"><span class="n" style="color: #333;">P_coverage</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'bam_file'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Mapped sequence reads (.bam)"</span><span class="p">)</span></span>
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478
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480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"><span class="n" style="color: #333;">P_coverage</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'interval'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Intervals (.bed or .list)"</span><span class="p">)</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"><span class="n" style="color: #333;">P_coverage</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="LC482" 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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483
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"><span class="n" style="color: #333;">P_coverage</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--count'</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="LC484" 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;">"""Get read depths by counting read midpoints within each bin.</span></span>
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481
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"><span class="s" style="color: #d14;"> (An alternative algorithm)."""</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#b1c2e997cbcbc150dfbb18cabfe5fbefc6fe41ce"><strong>cnvlib/coverage.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">@@ -17,19 +17,19 @@ from .parallel import rm, to_chunks</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.params</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NULL_LOG2_COVERAGE</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">processes</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="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">processes</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">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></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;">"""Calculate coverage in the given regions from BAM read depths."""</span></span>
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<pre style="margin: 0;">-<span id="LC22" 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;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">ensure_bam_sorted</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC22" 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;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">ensure_bam_sorted</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span><span class="s" style="color: #d14;">"BAM file %s must be sorted by coordinates"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">ensure_bam_index</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">)</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;"># ENH: count importers.TOO_MANY_NO_COVERAGE & warn</span></span>
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<pre style="margin: 0;"> <span id="LC27" 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;">interval_coverages</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cnarr</span></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>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">interval_coverages</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</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="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">interval_coverages</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_count</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate log2 coverages in the BAM file at each interval."""</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">meta</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'sample_id'</span><span class="p">:</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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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</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">@@ -47,7 +47,7 @@ def interval_coverages(bed_fname, bam_fname, by_count, min_mapq, processes):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Calculate average read depth in each bin</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">by_count</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;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interval_coverages_count</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></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;">read_counts</span><span class="p">,</span> <span class="n" style="color: #333;">cna_rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">results</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;">read_counts</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;">Series</span><span class="p">(</span><span class="n" style="color: #333;">read_counts</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;">cnarr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CNA</span><span class="p">.</span><span class="n" style="color: #333;">from_rows</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">cna_rows</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">@@ -55,8 +55,8 @@ def interval_coverages(bed_fname, bam_fname, by_count, min_mapq, processes):</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">meta_dict</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">meta</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" 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="LC57" 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;">interval_coverages_pileup</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">read_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">get_read_length</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">processes</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">read_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">get_read_length</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">read_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'basecount'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">read_len</span></span>
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<pre style="margin: 0;"> <span id="LC61" 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;">drop</span><span class="p">(</span><span class="s" style="color: #d14;">'basecount'</span><span class="p">,</span> <span class="n" style="color: #333;">axis</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="LC62" 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;">CNA</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">meta</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">@@ -75,7 +75,7 @@ def interval_coverages(bed_fname, bam_fname, by_count, min_mapq, processes):</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">tot_reads</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;">read_counts</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">read_counts</span><span class="p">.</span><span class="nb" style="color: #0086b3;">min</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">read_counts</span><span class="p">.</span><span class="nb" style="color: #0086b3;">max</span><span class="p">())</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">tot_mapped_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">bam_total_reads</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">tot_mapped_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samutil</span><span class="p">.</span><span class="n" style="color: #333;">bam_total_reads</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tot_mapped_reads</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <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="s" style="color: #d14;">"Percent reads in regions: %.3f (of %d mapped)"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="mf" style="color: #099;">100.</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tot_reads</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">tot_mapped_reads</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">@@ -86,11 +86,11 @@ def interval_coverages(bed_fname, bam_fname, by_count, min_mapq, processes):</td>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cnarr</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">interval_coverages_count</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span> <span class="n" style="color: #333;">procs</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="LC89" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">interval_coverages_count</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span> <span class="n" style="color: #333;">procs</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">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate log2 coverages in the BAM file at each interval."""</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">regions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tabio</span><span class="p">.</span><span class="n" style="color: #333;">read_auto</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">procs</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="LC93" class="line" lang="python"> <span class="n" style="color: #333;">bamfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">bamfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference_filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC94" 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;">subregions</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">regions</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="LC95" class="line" lang="python"> <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="s" style="color: #d14;">"Processing chromosome %s of %s"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<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 interval_coverages_count(bed_fname, bam_fname, min_mapq, procs=1):</td>
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98
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98
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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="p">[</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">row</span><span class="p">]</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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100
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">futures</span><span class="p">.</span><span class="n" style="color: #333;">ProcessPoolExecutor</span><span class="p">(</span><span class="n" style="color: #333;">procs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pool</span><span class="p">:</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">args_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">subr</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">args_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">subr</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_c</span><span class="p">,</span> <span class="n" style="color: #333;">subr</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">regions</span><span class="p">.</span><span class="n" style="color: #333;">by_chromosome</span><span class="p">())</span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chunk</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">_rdc</span><span class="p">,</span> <span class="n" style="color: #333;">args_iter</span><span class="p">):</span></span>
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104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">chunk</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,9 +110,9 @@ def _rdc(args):</td>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">_rdc_chunk</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">))</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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112
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_rdc_chunk</span><span class="p">(</span><span class="n" style="color: #333;">bamfile</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">):</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_rdc_chunk</span><span class="p">(</span><span class="n" style="color: #333;">bamfile</span><span class="p">,</span> <span class="n" style="color: #333;">regions</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">bamfile</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">bamfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bamfile</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">bamfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bamfile</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference_filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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116
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116
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<pre style="margin: 0;"> <span id="LC116" 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;">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="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">regions</span><span class="p">.</span><span class="n" style="color: #333;">coords</span><span class="p">([</span><span class="s" style="color: #d14;">"gene"</span><span class="p">]):</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">region_depth_count</span><span class="p">(</span><span class="n" style="color: #333;">bamfile</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 class="n" style="color: #333;">min_mapq</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" 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">@@ -152,15 +152,15 @@ def region_depth_count(bamfile, chrom, start, end, gene, min_mapq):</td>
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">row</span></span>
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>
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154
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">interval_coverages_pileup</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span> <span class="n" style="color: #333;">procs</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="LC155" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">interval_coverages_pileup</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">,</span> <span class="n" style="color: #333;">procs</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">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate log2 coverages in the BAM file at each interval."""</span></span>
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157
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <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="s" style="color: #d14;">"Processing reads in %s"</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">))</span></span>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">procs</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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159
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<pre style="margin: 0;">-<span id="LC159" 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;">bedcov</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC159" 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;">bedcov</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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161
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">chunks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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162
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">futures</span><span class="p">.</span><span class="n" style="color: #333;">ProcessPoolExecutor</span><span class="p">(</span><span class="n" style="color: #333;">procs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pool</span><span class="p">:</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;">args_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">bed_chunk</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">)</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;">args_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">bed_chunk</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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164
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">bed_chunk</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">to_chunks</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">))</span></span>
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165
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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;">for</span> <span class="n" style="color: #333;">bed_chunk_fname</span><span class="p">,</span> <span class="n" style="color: #333;">table</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">_bedcov</span><span class="p">,</span> <span class="n" style="color: #333;">args_iter</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;">chunks</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">table</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">@@ -189,7 +189,7 @@ def _bedcov(args):</td>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">table</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"></span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bedcov</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p">):</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bedcov</span><span class="p">(</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">min_mapq</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="s" style="color: #d14;">"""Calculate depth of all regions in a BED file via samtools (pysam) bedcov.</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;"> i.e. mean pileup depth across each region.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" 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="198" 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">@@ -198,6 +198,8 @@ def bedcov(bed_fname, bam_fname, min_mapq):</td>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">bed_fname</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">]</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_mapq</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">min_mapq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</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;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">'-Q'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">bytes</span><span class="p">(</span><span class="n" style="color: #333;">min_mapq</span><span class="p">)])</span></span>
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201
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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;">fasta</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="s" style="color: #d14;">'--reference'</span><span class="p">,</span> <span class="n" style="color: #333;">fasta</span><span class="p">])</span></span>
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201
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">bedcov</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">split_lines</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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203
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">SamtoolsError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">exc</span><span class="p">:</span></span>
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<li id="e0b9b6c135ef19da5b4d4718f3f11edff2251b58">
<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#e0b9b6c135ef19da5b4d4718f3f11edff2251b58"><strong>cnvlib/export.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">@@ -28,7 +28,7 @@ def merge_samples(filenames):</td>
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28
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<pre style="margin: 0;"> <span id="LC28" 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;">filenames</span><span class="p">:</span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">first_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;">filenames</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">out_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_cnarr</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">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"chromosome"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"start"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"gene"</span></span><span class="p"><span class="idiff right">]]</span></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">out_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_cnarr</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">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"chromosome"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"start"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"gene"</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">out_table</span><span class="p">[</span><span class="s" style="color: #d14;">"label"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">label_with_gene</span><span class="p">(</span><span class="n" style="color: #333;">first_cnarr</span><span class="p">)</span></span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">out_table</span><span class="p">[</span><span class="n" style="color: #333;">first_cnarr</span><span class="p">.</span><span class="n" style="color: #333;">sample_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">first_cnarr</span><span class="p">[</span><span class="s" style="color: #d14;">"log2"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC34" 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;">filenames</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" 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="101" 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">@@ -101,7 +101,7 @@ def export_nexus_basic(cnarr):</td>
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101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> Only represents one sample per file.</span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">out_table</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;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gene'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'log2'</span></span><span class="p"><span class="idiff right">]]</span></span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">out_table</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;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'gene'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'log2'</span></span><span class="p"><span class="idiff right">])</span></span></span>
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105
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">out_table</span><span class="p">[</span><span class="s" style="color: #d14;">'probe'</span><span class="p">]</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;">labels</span><span class="p">()</span></span>
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106
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">out_table</span></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" 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="123" 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">@@ -123,7 +123,7 @@ def export_nexus_ogt(cnarr, varr, min_weight=0.0):</td>
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123
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">bafs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">varr</span><span class="p">.</span><span class="n" style="color: #333;">baf_by_ranges</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">)</span></span>
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124
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <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="s" style="color: #d14;">"Placed %d variants into %d bins"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</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;">isnan</span><span class="p">(</span><span class="n" style="color: #333;">bafs</span><span class="p">)),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">))</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">out_table</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;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'log2'</span></span><span class="p"><span class="idiff right">]]</span></span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">out_table</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;">data</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'log2'</span></span><span class="p"><span class="idiff right">])</span></span></span>
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127
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">out_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_table</span><span class="p">.</span><span class="n" style="color: #333;">rename</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>
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128
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">"chromosome"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Chromosome"</span><span class="p">,</span></span>
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129
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">"start"</span><span class="p">:</span> <span class="s" style="color: #d14;">"Position"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="175" 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="175" 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">@@ -175,7 +175,7 @@ def export_bed(segments, ploidy, is_reference_male, is_sample_female,</td>
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175
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"><span class="s" style="color: #d14;"> If show="variant", skip regions where copy number is neutral, i.e. equal to</span></span>
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176
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"><span class="s" style="color: #d14;"> the reference ploidy on autosomes, or half that on sex chromosomes.</span></span>
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177
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"><span class="s" style="color: #d14;"> """</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;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segments</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">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"chromosome"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"start"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff right">]]</span></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;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segments</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">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"chromosome"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"start"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff right">])</span></span></span>
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179
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">"label"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">label</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">label</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">segments</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">]</span></span>
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180
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="s" style="color: #d14;">"ncopies"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">segments</span><span class="p">[</span><span class="s" style="color: #d14;">"cn"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"cn"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">segments</span></span>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">call</span><span class="p">.</span><span class="n" style="color: #333;">absolute_pure</span><span class="p">(</span><span class="n" style="color: #333;">segments</span><span class="p">,</span> <span class="n" style="color: #333;">ploidy</span><span class="p">,</span> <span class="n" style="color: #333;">is_reference_male</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="263" 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">@@ -263,7 +263,7 @@ def assign_ci_start_end(segarr, cnarr):</td>
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263
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"></span>
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264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">segments2vcf</span><span class="p">(</span><span class="n" style="color: #333;">segments</span><span class="p">,</span> <span class="n" style="color: #333;">ploidy</span><span class="p">,</span> <span class="n" style="color: #333;">is_reference_male</span><span class="p">,</span> <span class="n" style="color: #333;">is_sample_female</span><span class="p">):</span></span>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <span class="s" style="color: #d14;">"""Convert copy number segments to VCF records."""</span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">out_dframe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segments</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">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"chromosome"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"log2"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"probes"</span></span><span class="p"><span class="idiff right">]]</span></span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">out_dframe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segments</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">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"chromosome"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"log2"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"probes"</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">out_dframe</span><span class="p">[</span><span class="s" style="color: #d14;">"start"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">segments</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC269" 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;">in</span> <span class="n" style="color: #333;">segments</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="421" 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="421" 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">@@ -421,7 +421,7 @@ def export_theta(tumor_segs, normal_cn):</td>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">normal_cn</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">normal_cn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normal_cn</span><span class="p">.</span><span class="n" style="color: #333;">autosomes</span><span class="p">(</span><span class="n" style="color: #333;">also</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">xy_names</span><span class="p">)</span></span>
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC424" 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;">tumor_segs</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">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"start"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff right">]]</span></span></span>
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<pre style="margin: 0;">+<span id="LC424" 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;">tumor_segs</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">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"start"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"end"</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Convert chromosome names to 1-based integer indices</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">chr2idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">c</span><span class="p">:</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="534" 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">@@ -534,9 +534,9 @@ def export_theta_snps(varr):</td>
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">depth_key</span><span class="p">,</span> <span class="n" style="color: #333;">alt_key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">((</span><span class="s" style="color: #d14;">"depth"</span><span class="p">,</span> <span class="s" style="color: #d14;">"alt_count"</span><span class="p">),</span></span>
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"n_depth"</span><span class="p">,</span> <span class="s" style="color: #d14;">"n_alt_count"</span><span class="p">)):</span></span>
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Extract the SNP allele counts that THetA2 uses</span></span>
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<pre style="margin: 0;">-<span id="LC537" 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;">varr</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">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">depth_key</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt_key</span></span><span class="p"><span class="idiff right">)]</span></span></span>
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<pre style="margin: 0;">+<span id="LC537" 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;">varr</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">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">depth_key</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt_key</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"> <span class="n" style="color: #333;">table</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;">assign</span><span class="p">(</span><span class="n" style="color: #333;">ref_depth</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;">depth_key</span><span class="p">]</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;">alt_key</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">loc</span></span><span class="p"><span class="idiff">[:,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'ref_depth'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt_key</span></span><span class="p"><span class="idiff right">)]</span></span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">reindex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">columns</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'ref_depth'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt_key</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"> <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'ref_depth'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'ref_depth'</span><span class="p">].</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="s" style="color: #d14;">'int'</span><span class="p">)</span></span>
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">alt_key</span><span class="p">]</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;">alt_key</span><span class="p">].</span><span class="n" style="color: #333;">astype</span><span class="p">(</span><span class="s" style="color: #d14;">'int'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#6a9840d2eac663f8ebd4f5d048ee6f9ee950255b"><strong>cnvlib/fix.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">@@ -82,23 +82,29 @@ def load_adjust_coverages(cnarr, ref_cnarr, skip_low,</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: most bins have no or very low coverage; "</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">"check that the right BED file was used"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC84" 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="LC85" class="line" lang="python"> <span class="n" style="color: #333;">cnarr_index_reset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fix_gc</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'gc'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_matched</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <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="s" style="color: #d14;">"Correcting for GC bias..."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC89" 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;">center_by_window</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">,</span> <span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ref_matched</span><span class="p">[</span><span class="s" style="color: #d14;">'gc'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">cnarr_index_reset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC91" 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="LC92" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: Skipping correction for GC bias"</span><span class="p">)</span></span>
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91
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fix_edge</span><span class="p">:</span></span>
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92
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <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="s" style="color: #d14;">"Correcting for density bias..."</span><span class="p">)</span></span>
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93
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">edge_bias</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_edge_bias</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">INSERT_SIZE</span><span class="p">)</span></span>
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94
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96
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<pre style="margin: 0;"> <span id="LC96" 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;">center_by_window</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">,</span> <span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">edge_bias</span><span class="p">)</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">cnarr_index_reset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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98
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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;">fix_rmask</span><span class="p">:</span></span>
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96
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'rmask'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref_matched</span><span class="p">:</span></span>
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97
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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;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Correcting for RepeatMasker bias..."</span><span class="p">)</span></span>
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98
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101
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<pre style="margin: 0;"> <span id="LC101" 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;">center_by_window</span><span class="p">(</span><span class="n" style="color: #333;">cnarr</span><span class="p">,</span> <span class="p">.</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ref_matched</span><span class="p">[</span><span class="s" style="color: #d14;">'rmask'</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;">cnarr_index_reset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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99
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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100
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"WARNING: Skipping correction for "</span></span>
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101
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="s" style="color: #d14;">"RepeatMasker bias"</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cnarr_index_reset</span><span class="p">:</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">ref_matched</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">reset_index</span><span class="p">(</span><span class="n" style="color: #333;">drop</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;">inplace</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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102
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cnarr</span><span class="p">,</span> <span class="n" style="color: #333;">ref_matched</span></span>
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103
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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104
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#53cf62a516f30d088c59651d6a2d958620dd5fbc"><strong>cnvlib/rna.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">@@ -264,7 +264,7 @@ def align_gene_info_to_samples(gene_info, sample_counts, tx_lengths,</td>
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264
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># expression should be similar in male and female samples, i.e. neutral is 0</span></span>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"> <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="s" style="color: #d14;">"Weighting genes with below-average read counts"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">gene_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">axis</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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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">((</span><span class="n" style="color: #333;">gene_counts</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gene_counts</span><span class="p">.</span><span class="n" style="color: #333;">quantile</span><span class="p">(.</span><span class="mi" style="color: #099;">75</span><span class="p">)).</span><span class="n" style="color: #333;">clip<span class="idiff left">_upper</span></span><span class="p"><span class="idiff right">(</span></span><span class="mi" style="color: #099;">1</span><span class="p">))]</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">weights</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">sqrt</span><span class="p">((</span><span class="n" style="color: #333;">gene_counts</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">gene_counts</span><span class="p">.</span><span class="n" style="color: #333;">quantile</span><span class="p">(.</span><span class="mi" style="color: #099;">75</span><span class="p">)).</span><span class="n" style="color: #333;">clip</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">upper</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="mi" style="color: #099;">1</span><span class="p">))]</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"></span>
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269
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <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="s" style="color: #d14;">"Calculating normalized gene read depths"</span><span class="p">)</span></span>
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270
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">sample_depths_log2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normalize_read_depths</span><span class="p">(</span><span class="n" style="color: #333;">sc</span><span class="p">.</span><span class="n" style="color: #333;">divide</span><span class="p">(</span><span class="n" style="color: #333;">gi</span><span class="p">[</span><span class="s" style="color: #d14;">'tx_length'</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">@@ -328,7 +328,7 @@ def normalize_read_depths(sample_depths, normal_ids):</td>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">use_median</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Simple approach: divide normalized (1=neutral) values by gene medians</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">normal_avg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">normal_depths</span><span class="p">.</span><span class="n" style="color: #333;">median</span><span class="p">(</span><span class="n" style="color: #333;">axis</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="LC331" class="line" lang="python"> <span class="n" style="color: #333;">sample_depths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_depths</span><span class="p">.</span><span class="n" style="color: #333;">divide</span><span class="p">(</span><span class="n" style="color: #333;">normal_avg</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">clip<span class="idiff left">_lower</span></span><span class="p"><span class="idiff right">(</span></span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">sample_depths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_depths</span><span class="p">.</span><span class="n" style="color: #333;">divide</span><span class="p">(</span><span class="n" style="color: #333;">normal_avg</span><span class="p">,</span> <span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">clip</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">lower</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC332" 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="LC333" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Alternate approach: divide their IQR</span></span>
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># At each gene, sample depths above the normal sample depth 75%ile</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#042ad1cb073aba7f730f360c07cf2df6491e983a"><strong>cnvlib/samutil.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">@@ -10,13 +10,13 @@ from io import StringIO</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span><span class="p">,</span><span class="n" style="color: #333;">PurePath</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">drop_unmapped</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="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">drop_unmapped</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></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;">"""Get chromosome names, lengths, and number of mapped/unmapped reads.</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 class="s" style="color: #d14;"> Use the BAM index (.bai) to get the number of reads and size of each</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;"> chromosome. Contigs with no mapped reads are skipped.</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="n" style="color: #333;">handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">split_lines</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="LC19" class="line" lang="python"> <span class="n" style="color: #333;">handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">split_lines</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference_filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC20" 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;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">handle</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="n" style="color: #333;">header</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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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">names</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;">'length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mapped'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unmapped'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">drop_unmapped</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">@@ -24,12 +24,12 @@ def idxstats(bam_fname, drop_unmapped=False):</td>
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<pre style="margin: 0;"> <span id="LC24" 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="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bam_total_reads</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bam_total_reads</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"""Count the total number of mapped reads in a BAM file.</span></span>
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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 class="s" style="color: #d14;"> Uses the BAM index to do this quickly.</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC32" 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;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">drop_unmapped</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="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idxstats</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">drop_unmapped</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></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;">return</span> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">mapped</span><span class="p">.</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC35" 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">@@ -70,7 +70,7 @@ def ensure_bam_index(bam_fname):</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bai_fname</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ensure_bam_sorted</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ensure_bam_sorted</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">by_name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test if the reads in a BAM file are sorted as expected.</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> by_name=True: reads are expected to be sorted by query name. Consecutive</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">@@ -92,7 +92,7 @@ def ensure_bam_sorted(bam_fname, by_name=False, span=50):</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">prev</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;">pos</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ENH - repeat at 50%, ~99% through the BAM</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference_filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">last_read</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="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">islice</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="p">):</span></span>
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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;">out_of_order</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">last_read</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,7 +109,7 @@ def is_newer_than(target_fname, orig_fname):</td>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">target_fname</span><span class="p">).</span><span class="n" style="color: #333;">st_mtime</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">orig_fname</span><span class="p">).</span><span class="n" style="color: #333;">st_mtime</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_read_length</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_read_length</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get (median) read length from first few reads in a BAM file.</span></span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"><span class="s" style="color: #d14;"> Illumina reads all have the same length; other sequencers might not.</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">@@ -123,7 +123,7 @@ def get_read_length(bam, span=1000):</td>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">was_open</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference_filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC127" 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="LC128" class="line" lang="python"> <span class="n" style="color: #333;">was_open</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">islice</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">span</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#2b33ccf937d24b40fb7480b3013a15978923df38"><strong>cnvlib/segmentation/__init__.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">@@ -158,7 +158,10 @@ def _do_segmentation(cnarr, method, threshold, variants=None,</td>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">temp_write_text</span><span class="p">(</span><span class="n" style="color: #333;">rscript</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">script_strings</span><span class="p">,</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w+t'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">script_fname</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">seg_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">call_quiet</span><span class="p">(</span><span class="n" style="color: #333;">rscript_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'--vanilla'</span><span class="p">,</span> <span class="n" style="color: #333;">script_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">seg_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">call_quiet</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="LC162" class="line" lang="python"> <span class="s" style="color: #d14;">"--no-restore"</span><span class="p">,</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="s" style="color: #d14;">"--no-environ"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">script_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Convert R dataframe contents (SEG) to a proper CopyNumArray</span></span>
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># NB: Automatically shifts 'start' back from 1- to 0-indexed</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">segarr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tabio</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">StringIO</span><span class="p">(</span><span class="n" style="color: #333;">seg_out</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">()),</span> <span class="s" style="color: #d14;">"seg"</span><span class="p">,</span> <span class="n" style="color: #333;">into</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CNA</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#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">18</span>.04</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">20</span>.04</span></span>
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2
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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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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker"></span>
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4
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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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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="o" style="font-weight: 600;">&&</span> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> r-base-core</span>
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6
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<pre style="margin: 0;">-<span id="LC6" 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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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="docker"></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="o" style="font-weight: 600;">&&</span> apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-y</span> <span class="se" style="color: #d14;">\</span></span>
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9
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="docker"> liblzma-dev <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="docker"> python3-biopython <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="docker"> python3-dev <span class="se" style="color: #d14;">\</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">@@ -15,10 +12,12 @@ RUN apt-get install -y \</td>
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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-tk <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC15" 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="LC16" class="line" lang="docker"> zlib1g-dev</span>
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<pre style="margin: 0;">+<span id="LC17" 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="LC21" 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 class="idiff left right">.b1</span></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="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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<li id="9fa936d3ed63d2a4fe12751cc15f211fdcc8a505">
<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#9fa936d3ed63d2a4fe12751cc15f211fdcc8a505"><strong>scripts/cnv_expression_correlate.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">@@ -54,7 +54,7 @@ def correlate_cnv_expression(cnv_fname, expression_fname):</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">"kendall_t"</span><span class="p">:</span> <span class="n" style="color: #333;">tau</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="s" style="color: #d14;">"pearson_r"</span><span class="p">:</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="s" style="color: #d14;">"spearman_r"</span><span class="p">:</span> <span class="n" style="color: #333;">rho</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cnv_table</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">).</span><span class="n" style="color: #333;">clip<span class="idiff left">_lower</span></span><span class="p"><span class="idiff right">(</span></span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">fillna</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="p">},</span> <span class="n" style="color: #333;">index</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cnv_table</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">).</span><span class="n" style="color: #333;">clip</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">lower</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">fillna</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'hugo_gene'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">cnv_table</span><span class="p">[</span><span class="s" style="color: #d14;">'Hugo_Symbol'</span><span class="p">].</span><span class="n" style="color: #333;">fillna</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">).</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#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">@@ -36,7 +36,7 @@ logging.basicConfig(level=logging.INFO, format="%(message)s")</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ___________________________________________</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;"># Guided method: guess from potential targets</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_targets</span><span class="p">(</span><span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_bams</span><span class="p">,</span> <span class="n" style="color: #333;">procs</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_targets</span><span class="p">(</span><span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">sample_bams</span><span class="p">,</span> <span class="n" style="color: #333;">procs</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check if each potential target has significant coverage."""</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">baits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tabio</span><span class="p">.</span><span class="n" style="color: #333;">read</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,7 +47,7 @@ def filter_targets(target_bed, sample_bams, procs):</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">total_depths</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;">zeros</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">baits</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</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;">float_</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;">for</span> <span class="n" style="color: #333;">bam_fname</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sample_bams</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;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Evaluating targets in %s"</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnvlib</span><span class="p">.</span><span class="n" style="color: #333;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">procs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">sample</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cnvlib</span><span class="p">.</span><span class="n" style="color: #333;">do_coverage</span><span class="p">(</span><span class="n" style="color: #333;">target_bed</span><span class="p">,</span> <span class="n" style="color: #333;">bam_fname</span><span class="p">,</span> <span class="n" style="color: #333;">processes</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">procs</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fasta</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sample</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;">baits</span><span class="p">),</span> \</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"%d != %d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sample</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">baits</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;">total_depths</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">sample</span><span class="p">[</span><span class="s" style="color: #d14;">'depth'</span><span class="p">].</span><span class="n" style="color: #333;">values</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">@@ -204,6 +204,8 @@ 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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205
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205
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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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206
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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_coverage</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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207
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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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208
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210
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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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209
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">AP_x</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-t'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--targets'</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;">'TARGET_BED'</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">@@ -241,7 +243,7 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">processes</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="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC245" 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;">targets</span><span class="p">:</span></span>
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244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">baits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_targets</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">targets</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample_bams</span><span class="p">,</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="LC246" class="line" lang="python"> <span class="n" style="color: #333;">baits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_targets</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">targets</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample_bams</span><span class="p">,</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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fasta</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC247" 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="LC248" class="line" lang="python"> <span class="n" style="color: #333;">baits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">scan_targets</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">access</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">sample_bams</span><span class="p">,</span></span>
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247
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="mf" style="color: #099;">0.5</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;">min_depth</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># More sensitive 1st pass</span></span>
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<li id="af4aa75c1234fedbcee4a101a5adfd3e5b9a9570">
<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#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">@@ -76,7 +76,14 @@ def into_ranges(source, dest, src_col, default, summary_func):</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">iter_ranges</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="s" style="color: #d14;">"""Iterate through sub-ranges."""</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mode</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'inner'</span><span class="p">,</span> <span class="s" style="color: #d14;">'outer'</span><span class="p">,</span> <span class="s" style="color: #d14;">'trim'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">region_idx</span><span class="p">,</span> <span class="n" style="color: #333;">start_val</span><span class="p">,</span> <span class="n" style="color: #333;">end_val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idx_ranges</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Optional if we've already subsetted by chromosome (not checked!)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># ENH: accept array?</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC83" 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;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'chromosome'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chrom</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">(</span><span class="s" style="color: #d14;">"Chromosome %s is not in this probe set"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">chrom</span><span class="p">)</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;">region_idx</span><span class="p">,</span> <span class="n" style="color: #333;">start_val</span><span class="p">,</span> <span class="n" style="color: #333;">end_val</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idx_ranges</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">'inner'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'inner'</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'outer'</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">subtable</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;">iloc</span><span class="p">[</span><span class="n" style="color: #333;">region_idx</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'trim'</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,26 +111,22 @@ def iter_slices(table, other, mode, keep_empty):</td>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">bin_rows</span><span class="p">)):</span></span>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">Int64Index</span><span class="p">([])</span></span>
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106
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113
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<pre style="margin: 0;"> <span id="LC113" 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="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">slc</span><span class="p">,</span> <span class="n" style="color: #333;">_s</span><span class="p">,</span> <span class="n" style="color: #333;">_e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idx_ranges</span><span class="p">(</span><span class="n" style="color: #333;">src_rows</span><span class="p">,</span> <span class="bp" style="color: #999;"><span class="idiff left">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">bin_rows</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">slc</span><span class="p">,</span> <span class="n" style="color: #333;">_s</span><span class="p">,</span> <span class="n" style="color: #333;">_e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idx_ranges</span><span class="p">(</span><span class="n" style="color: #333;">src_rows</span><span class="p">,</span> <span class="n" style="color: #333;">bin_rows</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">bin_rows</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC116" 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;">src_rows</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">slc</span><span class="p">].</span><span class="n" style="color: #333;">values</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep_empty</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">indices</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">idx_ranges</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">idx_ranges</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">starts</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">"""Iterate through sub-ranges."""</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">mode</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'inner'</span><span class="p">,</span> <span class="s" style="color: #d14;">'outer'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Optional if we've already subsetted by chromosome (not checked!)</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># ENH: accept array?</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC121" 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;">table</span><span class="p">[</span><span class="s" style="color: #d14;">'chromosome'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">chrom</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">(</span><span class="s" style="color: #d14;">"Chromosome %s is not in this probe set"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">chrom</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Edge cases</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Edge cases: when the `table` is either empty, or both `starts` and `ends` are None, we want to signal the calling</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># function to use the entire table. To do this, we return slice(None), which, when passed to either .loc or .iloc,</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># will do just this. We cannot pass table.index to accomplish this because it will not work with .iloc if the table</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># is already subset by chromosome.</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</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 class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">starts</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">ends</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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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;"><span class="idiff left">table</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">index</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">slice</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>
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127
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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128
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Don't be fooled by nested bins</span></span>
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129
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132
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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="p">((</span><span class="n" style="color: #333;">ends</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</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;">ends</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#fcbc60e2d8cf298d97237ae8dd207f0f0eb8ba25"><strong>skgenome/tabio/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" 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="72" 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">@@ -72,7 +72,7 @@ def read(infile, fmt="tab", into=None, sample_id=None, meta=None, **kwargs):</td>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"sample_id"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sample_id</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">dframe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">io</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">common</span></span><span class="p">.</span><span class="n" style="color: #333;">EmptyDataError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">errors</span></span><span class="p">.</span><span class="n" style="color: #333;">EmptyDataError</span><span class="p">:</span></span>
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76
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># File is blank/empty, most likely</span></span>
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77
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <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="s" style="color: #d14;">"Blank %s file?: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">fmt</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">)</span></span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">dframe</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<a href="https://salsa.debian.org/med-team/cnvkit/-/commit/3c12d4a08092bebe7030f93e1fa365f5f2dc0745#91f24998b33057769876b12566e54d75ff87188d"><strong>skgenome/tabio/vcfsimple.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="91" 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">@@ -91,5 +91,5 @@ def set_ends(table):</td>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">alt_sz</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;">loc</span><span class="p">[</span><span class="n" style="color: #333;">need_end_idx</span><span class="p">,</span> <span class="s" style="color: #d14;">'alt'</span><span class="p">].</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="nb" style="color: #0086b3;">len</span><span class="p">()</span></span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">var_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alt_sz</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ref_sz</span></span>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO XXX if end > start, swap 'em?</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">var_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_sz</span><span class="p">.</span><span class="n" style="color: #333;">clip<span class="idiff left">_lower</span></span><span class="p"><span class="idiff right">(</span></span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">var_sz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">var_sz</span><span class="p">.</span><span class="n" style="color: #333;">clip</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">lower</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">need_end_idx</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;">table</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">need_end_idx</span><span class="p">,</span> <span class="s" style="color: #d14;">'start'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">var_sz</span></span></pre>
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