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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/hts-nim-tools">Debian Med / hts-nim-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/9dc6bcf7ef6dfb5bd593d48c1d8db136bb48675e">9dc6bcf7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-13T23:57:44+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.1</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1209052037a62cdff44ab08df446887d76a34e4f">
hts_nim_tools.nimble
</a>
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<li class="file-stats">
<a href="#f2c2f06077186afb15f4c6c83d18ffd9359b3e10">
src/copy_number_sampler.nim
</a>
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<h4>Changes:</h4>
<li id="1209052037a62cdff44ab08df446887d76a34e4f">
<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/9dc6bcf7ef6dfb5bd593d48c1d8db136bb48675e#1209052037a62cdff44ab08df446887d76a34e4f"><strong>hts_nim_tools.nimble</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Package</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">version = "0.2.<span class="idiff left right">0</span>"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">version = "0.2.<span class="idiff left right">1</span>"</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">author = "Brent Pedersen"</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">description = "hts-nim command-line tools"</span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">license = "MIT"</span>
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<li id="f2c2f06077186afb15f4c6c83d18ffd9359b3e10">
<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/9dc6bcf7ef6dfb5bd593d48c1d8db136bb48675e#f2c2f06077186afb15f4c6c83d18ffd9359b3e10"><strong>src/copy_number_sampler.nim</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="84" 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="84" 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">@@ -84,8 +84,8 @@ proc internal_sampler(ibam:Bam, obam:var Bam, regions:TableRef[string, seq[cnv]]</td>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="nim"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="nim"> <span class="k" style="font-weight: 600;">var</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">overlap_p</span><span class="p">(</span><span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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86
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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="nim"></span>
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<td class="diff-line-num old old_line" data-linenumber="87" 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">
87
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<td class="diff-line-num new_line old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rand<span class="idiff left right">om</span></span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">prob</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="88" 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">
88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">3.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rand<span class="idiff left right">om</span></span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rand</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">]</span><span class="p">.</span><span class="n" style="color: #333;">prob</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="nim"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">po</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">3.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rand</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span><span class="p">):</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="nim"> <span class="n" style="color: #333;">obam</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="nim"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="nim"></span>
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