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<h3>
Andreas Tille pushed to branch master
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/064d13a05e47d4a340dbbb54ed201fa4dc304112">064d13a0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-27T05:08:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.5.5.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/b6161e927440b921fb4abf6bc45a60b025fd5e86">b6161e92</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-27T05:08:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.5.5.2'
Update to upstream version '0.5.5.2'
with Debian dir fe56955d3ad058de805d3e9fd0497ac105e4906e</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/a2c508116ca116cadb0598b44355726087587761">a2c50811</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-27T05:09:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version closes #911874
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyfaidx/commit/4a9dc17a2b2c01c3d67168e90079c29efedc37ba">4a9dc17a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-27T05:14:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#83b1dda3455005121b48aadc1fefedc1b5e999ea">
pyfaidx/__init__.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/compare/e4da1ad0d1b2bd35a32dcba87569ca00f6f2d58f...4a9dc17a2b2c01c3d67168e90079c29efedc37ba#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: teal;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: teal;">sudo</span><span class="pi">:</span> <span class="no" style="color: teal;">false</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: teal;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</span></span>
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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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: teal;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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3
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<td class="diff-line-num new_line" data-linenumber="4" 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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"><span class="na" style="color: teal;">python</span><span class="pi">:</span></span>
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4
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<td class="diff-line-num new_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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">nightly'</span></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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.7'</span></span>
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5
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.6'</span></span>
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6
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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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.5'</span></span>
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7
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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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.4'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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="38" 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">@@ -36,7 +38,7 @@ deploy:</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"> <span class="na" style="color: teal;">secure</span><span class="pi">:</span> <span class="s" style="color: #d14;">MbSaeuitkVTZqxa0PJ3RcR1aMf+B/sMbcx2sWOo9xfLlRFDFpYWJZ0EfXWEhrVu2YWXpBsasgunTDWSi0jNcZMH92MzOC+UTVYr45LO5sy6hm4iSiAgm/DPgYWdjP0SFKr7eL/HWPS+gHvgkXL1upleX21O358bxaezoasuKFvs=</span></span>
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<td class="diff-line-num new_line" data-linenumber="39" 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="LC39" class="line" lang="yaml"> <span class="na" style="color: teal;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"> <span class="na" style="color: teal;">all_branches</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span>
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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="41" 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="LC39" class="line" lang="yaml"> <span class="na" style="color: teal;">python</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">2.7</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" 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="LC41" class="line" lang="yaml"> <span class="na" style="color: teal;">python</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">3.6</span></span></span>
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<td class="diff-line-num new_line" data-linenumber="42" 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="LC42" class="line" lang="yaml"> <span class="na" style="color: teal;">tags</span><span class="pi">:</span> <span class="no" style="color: teal;">true</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="yaml"> <span class="na" style="color: teal;">repo</span><span class="pi">:</span> <span class="s" style="color: #d14;">mdshw5/pyfaidx</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="yaml"><span class="na" style="color: teal;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-pyfaidx (0.5.5.<span class="idiff left right">1-1) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pyfaidx (0.5.5.<span class="idiff left right">2-1) unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #911874</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Secure URI in copyright format</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Thu, 25 Oct 2018 20:30:14</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Sat, 27 Oct 2018 07:11:40</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">python-pyfaidx (0.5.4-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<li id="83b1dda3455005121b48aadc1fefedc1b5e999ea">
<a href="https://salsa.debian.org/med-team/python-pyfaidx/compare/e4da1ad0d1b2bd35a32dcba87569ca00f6f2d58f...4a9dc17a2b2c01c3d67168e90079c29efedc37ba#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">@@ -25,7 +25,7 @@ if sys.version_info > (3, ):</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="n" style="color: #333;">dna_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</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="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC28" 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;">'0.5.5.<span class="idiff left right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC28" 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;">'0.5.5.<span class="idiff left right">2</span>'</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>
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<pre style="margin: 0;"> <span id="LC31" 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">@@ -813,7 +813,7 @@ class FastaRecord(object):</td>
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="python"> <span class="s" style="color: #d14;">""" Construct a line-based <span class="idiff left right">it</span>erator that respects the original line lengths. """</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="python"> <span class="s" style="color: #d14;">""" Construct a line-based <span class="idiff left right">gen</span>erator that respects the original line lengths. """</span></span>
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="python"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_fa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span></span>
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</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">@@ -822,11 +822,11 @@ class FastaRecord(object):</td>
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</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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<pre style="margin: 0;"> <span id="LC823" 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="LC824" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</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="LC825" class="line" lang="python"> <span class="k" style="font-weight: 600;">r<span class="idiff left">aise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">StopIteratio</span>n</span></span>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="python"> <span class="k" style="font-weight: 600;">r<span class="idiff left right">etur</span>n</span></span>
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">line_len</span></span>
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__reversed__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="s" style="color: #d14;">""" Reverse line-based <span class="idiff left right">it</span>erator """</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="python"> <span class="s" style="color: #d14;">""" Reverse line-based <span class="idiff left right">gen</span>erator """</span></span>
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_fa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lenc</span></span>
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># have to determine last line length</span></span>
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="python"> <span class="n" style="color: #333;">last_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">line_len</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">@@ -839,7 +839,7 @@ class FastaRecord(object):</td>
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</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="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="LC840" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="p">[:</span><span class="n" style="color: #333;">end</span><span class="p">][::</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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842
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="python"> <span class="k" style="font-weight: 600;">r<span class="idiff left">aise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">StopIteratio</span>n</span></span>
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="python"> <span class="k" style="font-weight: 600;">r<span class="idiff left right">etur</span>n</span></span>
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># first iteration</span></span>
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">last_line</span></span>
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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