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<h3>
Nilesh Patra pushed to branch master
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>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.1</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/e774ab44e8e9ad0603ad9726d38a630df791381b">e774ab44</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-13T23:57:44+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/61931e6ffbccc5e97666ca31d6b2ca0c7c070f17">61931e6f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-13T23:57:45+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.2.1'
Update to upstream version '0.2.1'
with Debian dir 7f8d335dca30179aa63906564907861d6ea68ef9</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/98db643b8b7b704bcb3967a87de36b736cc45a2a">98db643b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-13T23:58:50+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove patch since new release is tagged
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hts-nim-tools/-/commit/adc4aa02fa0f139a214c873543eff507130d85a9">adc4aa02</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-11-13T23:59:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#1ec66a592180b9e816019238bbe6d40c69baa20e">
<span class="deleted-file">
−
debian/patches/import_random.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="deleted-file">
−
debian/patches/series
</span>
</a>
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<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>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/compare/8e4f2076834c3d7d720def0b2727aa3902a77a5c...adc4aa02fa0f139a214c873543eff507130d85a9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hts-nim-tools (0.2.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num new new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Fri, 13 Nov 2020 23:59:28 +0530</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">hts-nim-tools (0.2.0-3) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> * Added dependency on nim-hts-dev, without which the library could</span>
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</li>
<li id="1ec66a592180b9e816019238bbe6d40c69baa20e">
<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/compare/8e4f2076834c3d7d720def0b2727aa3902a77a5c...adc4aa02fa0f139a214c873543eff507130d85a9#1ec66a592180b9e816019238bbe6d40c69baa20e"><strong>debian/patches/import_random.patch</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Reinstante compatibilitz with nim 1.4</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Forward: This is effectively a backport of a change I found in the current</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> github repository. I asked to tag a new release on</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> https://github.com/brentp/hts-nim-tools/issues/11</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Author: Steffen Moeller <moeller@debian.org></span></span>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">Index: hts-nim-tools/src/copy_number_sampler.nim</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hts-nim-tools.orig/src/copy_number_sampler.nim</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hts-nim-tools/src/copy_number_sampler.nim</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="p">@@ -6,6 +6,7 @@</span> import lapper</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> import strutils</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> import tables</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> import algorithm</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import random</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> import ./version</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -84,8 +85,8 @@</span> proc internal_sampler(ibam:Bam, obam:var</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> var po = overlap_p(res[0], record)</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if res[0].prob < 1 and random(1.0) < res[0].prob:</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if po == 1 or po < 3.0 * random(1.0):</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if res[0].prob < 1 and rand(1.0) < res[0].prob:</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if po == 1 or po < 3.0 * rand(1.0):</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> obam.write(record)</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> continue</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/compare/8e4f2076834c3d7d720def0b2727aa3902a77a5c...adc4aa02fa0f139a214c873543eff507130d85a9#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">import_random.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/compare/8e4f2076834c3d7d720def0b2727aa3902a77a5c...adc4aa02fa0f139a214c873543eff507130d85a9#1209052037a62cdff44ab08df446887d76a34e4f"><strong>hts_nim_tools.nimble</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># Package</span>
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2
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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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2
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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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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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<a href="https://salsa.debian.org/med-team/hts-nim-tools/-/compare/8e4f2076834c3d7d720def0b2727aa3902a77a5c...adc4aa02fa0f139a214c873543eff507130d85a9#f2c2f06077186afb15f4c6c83d18ffd9359b3e10"><strong>src/copy_number_sampler.nim</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">@@ -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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<pre style="margin: 0;"> <span id="LC84" class="line" lang="nim"></span>
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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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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">
87
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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">
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><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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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="nim"></span>
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