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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pyfaidx">Debian Med / python-pyfaidx</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/008eb56e8527dd1578c066f3a734dab683318b7a">008eb56e</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-12T18:30:05+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.5.9.2</pre>
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<h4>1 changed file:</h4>
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<a href="#83b1dda3455005121b48aadc1fefedc1b5e999ea">
pyfaidx/__init__.py
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<h4>Changes:</h4>
<li id="83b1dda3455005121b48aadc1fefedc1b5e999ea">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/-/commit/008eb56e8527dd1578c066f3a734dab683318b7a#83b1dda3455005121b48aadc1fefedc1b5e999ea"><strong>pyfaidx/__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">@@ -29,7 +29,7 @@ if sys.version_info > (3, ):</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">dna_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="p">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.5.9.<span class="idiff left right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">'0.5.9.<span class="idiff left right">2</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></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 class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">KeyFunctionError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</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">@@ -659,11 +659,12 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Calculate offset (https://github.com/samtools/htslib/blob/20238f354894775ed22156cdd077bc0d544fa933/faidx.c#L398)</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="n" style="color: #333;">newlines_before</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lenb</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lenc</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">newlines_to_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lenb</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lenc</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">newlines_to_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python"> <span class="n" style="color: #333;">newlines_inside</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newlines_to_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">newlines_before</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python"> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newlines_inside</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_len</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python"> <span class="n" style="color: #333;">bstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newlines_before</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start0</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"> <span class="n" style="color: #333;">newline_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">lenc</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newlines_inside</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">newline_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_len</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"> <span class="n" style="color: #333;">bstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newlines_before</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">newline_blen</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start0</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq_blen</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">strict_bounds</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FetchError</span><span class="p">(</span><span class="s" style="color: #d14;">"Requested coordinates start={0:n} end={1:n} are "</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"> <span class="s" style="color: #d14;">"invalid.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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>
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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">@@ -674,7 +675,7 @@ class Faidx(object):</td>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">lock</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_bgzf</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># We can't add to virtual offsets, so we need to read from the beginning of the record and trim the beginning if needed</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left">newlines_before</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">newlines_inside</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_len</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">newlines_before</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">newline_blen</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">newlines_inside</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">newline_blen</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_len</span></span>
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<pre style="margin: 0;"> <span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">chunk_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">).</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chunk_seq</span><span class="p">[</span><span class="n" style="color: #333;">start0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">newlines_before</span><span class="p">:]</span></span>
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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