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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/htseq">Debian Med / htseq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/cb923c31b4c6e074e4a5bfc951629e468d9ae492">cb923c31</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-28T17:25:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.10.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/fdb6174a67477223ffb280570749077ad8ed8f34">fdb6174a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-28T17:25:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.10.0'
Update to upstream version '0.10.0'
with Debian dir 88881e659deed05e40728e7f33cc3fd70b484498</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/89e0b76613584a8e82e46d3777ef54a007c6b39e">89e0b766</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-28T17:25:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/commit/ebb0d026ee514e57bb49f887ccf09bcd5129203a">ebb0d026</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-28T17:30:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
</a>
</li>
<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#eeecb7e0b0919e8015c422db84ad56111da921a7">
python2/HTSeq/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#e860acebd843648e033662eac1a1d0620e7dc6d7">
python2/HTSeq/_version.py
</a>
</li>
<li class="file-stats">
<a href="#48d1d1c7549dfe506a0f860bd23b62c026693628">
python2/HTSeq/scripts/count.py
</a>
</li>
<li class="file-stats">
<a href="#fc97c7539c2f5e31f663b33a263013f82d8eac33">
python2/src/HTSeq/_HTSeq.pyx
</a>
</li>
<li class="file-stats">
<a href="#5f8bf900fa412d21d637ab1c77a631a00551279d">
python3/HTSeq/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#6ef6a1ad5db69d445d8356610d7f345cb83afe6a">
python3/HTSeq/_version.py
</a>
</li>
<li class="file-stats">
<a href="#e5673f04e9098a0bf1f4da138b373b347616dfe0">
python3/HTSeq/scripts/count.py
</a>
</li>
<li class="file-stats">
<a href="#a8dcb9b2f363c919df57f4b82171ac5afa3861eb">
python3/src/HTSeq/_HTSeq.pyx
</a>
</li>
<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
setup.cfg
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Metadata-Version: <span class="idiff left right">1</span>.1</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Metadata-Version: <span class="idiff left right">2</span>.1</span>
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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="LC2" class="line" lang="plaintext">Name: HTSeq</span>
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<td class="diff-line-num old old_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">9.1</span></span>
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3
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.<span class="idiff left right">10.0</span></span>
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<td class="diff-line-num old_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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays</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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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/simon-anders/htseq</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Author: Fabio Zanini</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Author-email: fabio.zanini@stanford.edu</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Author: Simon Anders</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Author-email: sanders@fs.tum.de</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Maintainer: Fabio Zanini</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Maintainer-email: fabio.zanini@stanford.edu</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">License: GPL3</span>
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<td class="diff-line-num old_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="LC11" class="line" lang="plaintext">Description: </span>
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<td class="diff-line-num new_line" data-linenumber="12" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> A framework to process and analyze data from high-throughput sequencing</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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">@@ -21,3 +23,4 @@ Classifier: Intended Audience :: Science/Research</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Classifier: License :: OSI Approved :: GNU General Public License (GPL)</span>
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<td class="diff-line-num old_line" data-linenumber="22" 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="plaintext">Classifier: Operating System :: POSIX</span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Classifier: Programming Language :: Python</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Provides-Extra: htseq-qa</span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0.<span class="idiff left right">9.1</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0.<span class="idiff left right">10.0</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">htseq (0.10.0-1) unstable; 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"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 28 May 2018 17:26:34 +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">htseq (0.9.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#eeecb7e0b0919e8015c422db84ad56111da921a7"><strong>python2/HTSeq/__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">@@ -3,16 +3,19 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">See htseq.readthedocs.io/en/master/index.html for documentation.</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span><span class="p">,</span> <span class="n" style="color: #333;">warnings</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">,</span> <span class="n" style="color: #333;">shlex</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">itertools</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">warnings</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shlex</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" 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="LC9" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">_HTSeq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="idiff left right"> </span><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">_HTSeq</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isfile</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"setup.py"</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">raise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">ImportError</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"Cannot import 'HTSeq' when working directory is HTSeq's own build directory."</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;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">isfile</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"setup.py"</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">raise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">ImportError</span></span><span class="p"><span class="idiff right">(</span></span><span class="s" style="color: #d14;">"Cannot import 'HTSeq' when working directory is HTSeq's own build directory."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">_version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#from vcf_reader import *</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">@@ -22,420 +25,424 @@ from _version import __version__</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#########################</span></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>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FileOrSequence</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">object</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">""" The construcutor takes one argument, which may either be a string,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="s" style="color: #d14;"> which is interpreted as a file name (possibly with path), or a</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">connection, by which we mean a text file opened for reading, or </span></span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">any other object that can provide an iterator over strings </span></span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> (lines of the file).</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> The advantage of passing a file name instead of an already opened file</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> is that if an iterator is requested several times, the file will be</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> re-opened each time. If the file is already open, its lines can be read</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right">only once, and then, the iterator stays exhausted. </span></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> Furthermore, if a file name is passed that end in ".gz" or ".gzip"</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> (case insensitive), it is transparently gunzipped.</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">__init__</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="idiff"> </span><span class="p"><span class="idiff">):</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename_or_sequence</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</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="LC44" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="idiff right"> </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;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lower</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endswith</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">".gz"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">".gzip"</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </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;"><span class="idiff left">lines</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">gzip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'rt'</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC50" 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="LC51" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">lines</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" 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="LC53" class="line" lang="python"> <span class="n" style="color: #333;">lines</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;">fos</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="idiff right"> </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;">lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</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="LC60" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">__repr__</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s object, connected to file name '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__class__</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__name__</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC65" 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="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s object, connected to </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__class__</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__name__</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">repr</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">get_line_number_string</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</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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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s closed"</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;">fos</span></span>
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<pre style="margin: 0;">-<span id="LC73" 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="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"file closed"</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="idiff right"> </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;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"line </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d of file </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</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="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">line_no</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC77" 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="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"line </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d"</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;">line_no</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FileOrSequence</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">object</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="idiff left right"> </span><span class="s" style="color: #d14;">""" The construcutor takes one argument, which may either be a string,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> </span>which is interpreted as a file name (possibly with path), or a</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> connection, by which we mean a text file opened for reading, or</span></span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> any other object that can provide an iterator over strings</span></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> </span>(lines of the file).</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 class="s" style="color: #d14;"> <span class="idiff left right"> </span>The advantage of passing a file name instead of an already opened file</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> </span>is that if an iterator is requested several times, the file will be</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> </span>re-opened each time. If the file is already open, its lines can be read</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> only once, and then, the iterator stays exhausted.</span></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> </span>Furthermore, if a file name is passed that end in ".gz" or ".gzip"</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> </span>(case insensitive), it is transparently gunzipped.</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> <span class="idiff left right"> </span>"""</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">__init__</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="p"><span class="idiff right">):</span></span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename_or_sequence</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</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="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">basestring</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lower</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endswith</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">".gz"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">".gzip"</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">lines</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">gzip</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'rt'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">lines</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fos</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">lines</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;">fos</span></span>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">line</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">str</span></span><span class="p">):</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">lines</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="62" 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">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">__repr__</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">str</span></span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s object, connected to file name '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__class__</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__name__</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fos</span></span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s object, connected to </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__class__</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__name__</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">repr</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff right">))</span></span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">get_line_number_string</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_no</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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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">str</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s closed"</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;">fos</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"file closed"</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">str</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"line </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d of file </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s"</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="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">line_no</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fos</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"line </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d"</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;">line_no</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#########################</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## Features</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#########################</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="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GenomicFeature</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">object</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"""A genomic feature, i.e., an interval on a genome with metadata.</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> At minimum, the following information should be provided by slots:</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> name: a string identifying the feature (e.g., a gene symbol)</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> type: a string giving the feature type (e.g., "gene", "exon")</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> iv: a GenomicInterval object specifying the feature locus </span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">type_</span><span class="p">,</span> <span class="n" style="color: #333;">interval</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">intern</span><span class="p">(</span> <span class="n" style="color: #333;">type_</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interval</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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</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="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' at </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d -> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d (strand '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s')>"</span> <span class="o" style="font-weight: 600;">%</span> \</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <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;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</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>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_d</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_d</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</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;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">GenomicFeature</span> <span class="p">):</span></span>
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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="bp" style="color: #999;">False</span></span>
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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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span></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;">__neq__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC113" 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;">isinstance</span><span class="p">(</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">GenomicFeature</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__eq__</span><span class="p">(</span> <span class="n" style="color: #333;">other</span> <span class="p">)</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> </span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_gff_line</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">with_equal_sign</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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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">source</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;">source</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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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;">score</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;">score</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</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;">try</span><span class="p">:</span></span>
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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;">frame</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;">frame</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;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span></span>
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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;">try</span><span class="p">:</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">attr</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;">attr</span></span>
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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;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="s" style="color: #d14;">'ID'</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>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">with_equal_sign</span><span class="p">:</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"="</span></span>
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<pre style="margin: 0;">-<span id="LC136" 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="LC137" class="line" lang="python"> <span class="n" style="color: #333;">sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">attr_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'; '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="p">[</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span> <span class="n" style="color: #333;">ak</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">[</span><span class="n" style="color: #333;">ak</span><span class="p">]</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ak</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attr</span> <span class="p">]</span> <span class="p">)</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">source</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">score</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="n" style="color: #333;">attr_str</span> <span class="p">)</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> </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 class="n" style="color: #333;">_re_attr_main</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;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s*([^</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">=]+)[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s=]+(.*)"</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;">_re_attr_empty</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;">"^</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s*$"</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_GFF_attribute_string</span><span class="p">(</span> <span class="n" style="color: #333;">attrStr</span><span class="p">,</span> <span class="n" style="color: #333;">extra_return_first_value</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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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parses a GFF attribute string and returns it as a dictionary.</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> If 'extra_return_first_value' is set, a pair is returned: the dictionary</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> and the value of the first attribute. This might be useful if this is the ID.</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">attrStr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">):</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">attrStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attrStr</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="LC155" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">first_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"_unnamed_"</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">izip</span><span class="p">(</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(),</span> <span class="n" style="color: #333;">_HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quotesafe_split</span><span class="p">(</span> <span class="n" style="color: #333;">attrStr</span> <span class="p">)</span> <span class="p">):</span></span>
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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;">_re_attr_empty</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span> <span class="n" style="color: #333;">attr</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="k" style="font-weight: 600;">continue</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;">if</span> <span class="n" style="color: #333;">attr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span> <span class="s" style="color: #d14;">'"'</span> <span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="p">):</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"The attribute string seems to contain mismatched quotes."</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_attr_main</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span> <span class="n" style="color: #333;">attr</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="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">mo</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="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Failure parsing GFF attribute line"</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;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">'"'</span> <span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span> <span class="s" style="color: #d14;">'"'</span> <span class="p">):</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</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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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#val = urllib.unquote( val )</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span> <span class="nb" style="color: #0086b3;">intern</span><span class="p">(</span><span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">intern</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extra_return_first_value</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i</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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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">first_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span> </span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extra_return_first_value</span><span class="p">:</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">first_val</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC174" 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="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span></span>
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"><span class="n" style="color: #333;">_re_gff_meta_comment</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;">"##</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s*(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S+)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S*)"</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GFF_Reader</span><span class="p">(</span> <span class="n" style="color: #333;">FileOrSequence</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse a GFF file</span></span>
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"><span class="s" style="color: #d14;"> Pass the constructor either a file name or an iterator of lines of a </span></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"><span class="s" style="color: #d14;"> GFF files. If a file name is specified, it may refer to a gzip compressed</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"><span class="s" style="color: #d14;"> file.</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"><span class="s" style="color: #d14;"> Iterating over the object then yields GenomicFeature objects.</span></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span><span class="p">,</span> <span class="n" style="color: #333;">end_included</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="LC191" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_included</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_included</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC196" 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="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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;">continue</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">'#'</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;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"##"</span> <span class="p">):</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_gff_meta_comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span> <span class="n" style="color: #333;">line</span> <span class="p">)</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mo</span><span class="p">:</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GenomicFeature</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">"""A genomic feature, i.e., an interval on a genome with metadata.</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> At minimum, the following information should be provided by slots:</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> name: a string identifying the feature (e.g., a gene symbol)</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> type: a string giving the feature type (e.g., "gene", "exon")</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;"> iv: a GenomicInterval object specifying the feature locus</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">type_</span><span class="p">,</span> <span class="n" style="color: #333;">interval</span><span class="p">):</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">intern</span><span class="p">(</span><span class="n" style="color: #333;">type_</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interval</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' at </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d -> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d (strand '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s')>"</span> <span class="o" style="font-weight: 600;">%</span> \</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <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;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</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>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_d</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_d</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</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>
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>
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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;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">GenomicFeature</span><span class="p">):</span></span>
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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="bp" style="color: #999;">False</span></span>
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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;">return</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="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__neq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</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="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">GenomicFeature</span><span class="p">):</span></span>
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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;">return</span> <span class="bp" style="color: #999;">True</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__eq__</span><span class="p">(</span><span class="n" style="color: #333;">other</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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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_gff_line</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">with_equal_sign</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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120
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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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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">source</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;">source</span></span>
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122
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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;">AttributeError</span><span class="p">:</span></span>
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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;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">score</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;">score</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" 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">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</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;">try</span><span class="p">:</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">frame</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;">frame</span></span>
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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;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span></span>
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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;">try</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">attr</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;">attr</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'ID'</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>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">with_equal_sign</span><span class="p">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"="</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">attr_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'; '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">ak</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">[</span><span class="n" style="color: #333;">ak</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ak</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attr</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="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</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;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="n" style="color: #333;">attr_str</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"><span class="n" style="color: #333;">_re_attr_main</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;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s*([^</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">=]+)[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s=]+(.*)"</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="n" style="color: #333;">_re_attr_empty</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;">"^</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s*$"</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_GFF_attribute_string</span><span class="p">(</span><span class="n" style="color: #333;">attrStr</span><span class="p">,</span> <span class="n" style="color: #333;">extra_return_first_value</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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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parses a GFF attribute string and returns it as a dictionary.</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"><span class="s" style="color: #d14;"> If 'extra_return_first_value' is set, a pair is returned: the dictionary</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> and the value of the first attribute. This might be useful if this is the ID.</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">attrStr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">):</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;">attrStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attrStr</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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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</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;">first_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"_unnamed_"</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;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">itertools</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(),</span> <span class="n" style="color: #333;">_HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quotesafe_split</span><span class="p">(</span><span class="n" style="color: #333;">attrStr</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_re_attr_empty</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">attr</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="p">(</span> <span class="n" style="color: #333;">seqname</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">feature</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;">score</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="n" style="color: #333;">attributeStr</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</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="mi" style="color: #099;">8</span> <span class="p">)</span> </span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="p">(</span> <span class="n" style="color: #333;">attr</span><span class="p">,</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;">parse_GFF_attribute_string</span><span class="p">(</span> <span class="n" style="color: #333;">attributeStr</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_included</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span> <span class="n" style="color: #333;">seqname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</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 class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">),</span> <span class="n" style="color: #333;">strand</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC211" 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="LC212" class="line" lang="python"> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span> <span class="n" style="color: #333;">seqname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</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 class="nb" style="color: #0086b3;">int</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 class="n" style="color: #333;">strand</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicFeature</span><span class="p">(</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</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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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span> <span class="n" style="color: #333;">score</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">frame</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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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">frame</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;">frame</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attr</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_feature_dict</span><span class="p">(</span> <span class="n" style="color: #333;">feature_sequence</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="s" style="color: #d14;">"""A feature dict is a convenient way to organize a sequence of Feature </span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"><span class="s" style="color: #d14;"> object (which you have got, e.g., from parse_GFF).</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"><span class="s" style="color: #d14;"> The function returns a dict with all the feature types as keys. Each value</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"><span class="s" style="color: #d14;"> of this dict is again a dict, now of feature names. The values of this dict</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"><span class="s" style="color: #d14;"> is a list of feature.</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"><span class="s" style="color: #d14;"> An example makes this clear. Let's say you load the C. elegans GTF file</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"><span class="s" style="color: #d14;"> from Ensemble and make a feature dict:</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;"> >>> worm_features_dict = HTSeq.make_feature_dict( HTSeq.parse_GFF( </span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;"> ... "test_data/Caenorhabditis_elegans.WS200.55.gtf.gz" ) )</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"><span class="s" style="color: #d14;"> (This command may take a few minutes to deal with the 430,000 features</span></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"><span class="s" style="color: #d14;"> in the GTF file. Note that you may need a lot of RAM if you have millions</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"><span class="s" style="color: #d14;"> of features.)</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> Then, you can simply access, say, exon 0 of gene "F08E10.4" as follows:</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;"> >>> worm_features_dict[ 'exon' ][ 'F08E10.4' ][ 0 ]</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"><span class="s" style="color: #d14;"> <GenomicFeature: exon 'F08E10.4' at V: 17479353 -> 17479001 (strand '-')></span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">feature_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">res_ftype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res</span><span class="p">[</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res_ftype</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">res_ftype</span><span class="p">[</span> <span class="n" style="color: #333;">f</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="p">[</span> <span class="n" style="color: #333;">f</span> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC254" 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="LC255" class="line" lang="python"> <span class="n" style="color: #333;">res_ftype</span><span class="p">[</span> <span class="n" style="color: #333;">f</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;">append</span><span class="p">(</span> <span class="n" style="color: #333;">f</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">attr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"The attribute string seems to contain mismatched quotes."</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;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_attr_main</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">attr</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="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">mo</span><span class="p">:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Failure parsing GFF attribute line"</span><span class="p">)</span></span>
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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;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">val</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">):</span></span>
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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;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span><span class="p">[</span><span class="mi" style="color: #099;">1</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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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># val = urllib.unquote(val)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="nb" style="color: #0086b3;">intern</span><span class="p">(</span><span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">intern</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extra_return_first_value</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i</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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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">first_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">extra_return_first_value</span><span class="p">:</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">first_val</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</span></span>
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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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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"><span class="n" style="color: #333;">_re_gff_meta_comment</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;">"##</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s*(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S+)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">s+(</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s" style="color: #d14;">S*)"</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GFF_Reader</span><span class="p">(</span><span class="n" style="color: #333;">FileOrSequence</span><span class="p">):</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse a GFF file</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"><span class="s" style="color: #d14;"> Pass the constructor either a file name or an iterator of lines of a</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"><span class="s" style="color: #d14;"> GFF files. If a file name is specified, it may refer to a gzip compressed</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"><span class="s" style="color: #d14;"> file.</span></span>
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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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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;"> Iterating over the object then yields GenomicFeature objects.</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span><span class="p">,</span> <span class="n" style="color: #333;">end_included</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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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_included</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end_included</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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257
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"></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;">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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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
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;">line</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'#'</span><span class="p">):</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"##"</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_gff_meta_comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mo</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span><span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</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;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</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="k" style="font-weight: 600;">continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">seqname</span><span class="p">,</span> <span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">feature</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;">score</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" 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">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">frame</span><span class="p">,</span> <span class="n" style="color: #333;">attributeStr</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</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="mi" style="color: #099;">8</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" 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">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">attr</span><span class="p">,</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;">parse_GFF_attribute_string</span><span class="p">(</span><span class="n" style="color: #333;">attributeStr</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="212" 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">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_included</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" 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">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span><span class="n" style="color: #333;">seqname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</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 class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">),</span> <span class="n" style="color: #333;">strand</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="214" 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">
214
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<pre style="margin: 0;">+<span id="LC214" 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="LC215" class="line" lang="python"> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span><span class="n" style="color: #333;">seqname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start</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 class="nb" style="color: #0086b3;">int</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 class="n" style="color: #333;">strand</span><span class="p">)</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicFeature</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">feature</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="p">)</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">score</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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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">score</span><span class="p">)</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">frame</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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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">frame</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;">frame</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">source</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">source</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">frame</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attr</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_feature_dict</span><span class="p">(</span><span class="n" style="color: #333;">feature_sequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="s" style="color: #d14;">"""A feature dict is a convenient way to organize a sequence of Feature</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"><span class="s" style="color: #d14;"> object (which you have got, e.g., from parse_GFF).</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"><span class="s" style="color: #d14;"> The function returns a dict with all the feature types as keys. Each value</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"><span class="s" style="color: #d14;"> of this dict is again a dict, now of feature names. The values of this dict</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"><span class="s" style="color: #d14;"> is a list of feature.</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;"> An example makes this clear. Let's say you load the C. elegans GTF file</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;"> from Ensemble and make a feature dict:</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"><span class="s" style="color: #d14;"> >>> worm_features_dict = HTSeq.make_feature_dict(HTSeq.parse_GFF(</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"><span class="s" style="color: #d14;"> ... "test_data/Caenorhabditis_elegans.WS200.55.gtf.gz"))</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"><span class="s" style="color: #d14;"> (This command may take a few minutes to deal with the 430,000 features</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;"> in the GTF file. Note that you may need a lot of RAM if you have millions</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;"> of features.)</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="s" style="color: #d14;"> Then, you can simply access, say, exon 0 of gene "F08E10.4" as follows:</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;"> >>> worm_features_dict[ 'exon' ][ 'F08E10.4' ][ 0 ]</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;"> <GenomicFeature: exon 'F08E10.4' at V: 17479353 -> 17479001 (strand '-')></span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">feature_sequence</span><span class="p">:</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">res_ftype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res_ftype</span><span class="p">:</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">res_ftype</span><span class="p">[</span><span class="n" style="color: #333;">f</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="p">[</span><span class="n" style="color: #333;">f</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">res_ftype</span><span class="p">[</span><span class="n" style="color: #333;">f</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;">append</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#########################</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## GenomicArray</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#########################</span></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"></span>
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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;">read_chrom_lens</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delimiter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">dict</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">csv</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">reader</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delimiter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">delimiter</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">read_chrom_lens</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delimiter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">return</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">dict</span></span><span class="p"><span class="idiff">(((</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff right">))</span></span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">csv</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">reader</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delimiter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">delimiter</span></span><span class="p"><span class="idiff right">))</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#########################</span></span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## Sequence readers</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#########################</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"><span class="n" style="color: #333;">_re_fasta_header_line</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="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">r'>\s*(\S+)\s*(.*)'</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"><span class="n" style="color: #333;">_re_fasta_header_line</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;"><span class="idiff left">r'>\s*(\S+)\s*(.*)'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaReader</span><span class="p">(</span> <span class="n" style="color: #333;">FileOrSequence</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="s" style="color: #d14;">"""A Fasta_Reader is associated with a FASTA file or an open connection</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"><span class="s" style="color: #d14;"> to a file-like object with content in FASTA format.</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;"> It can generate an iterator over the sequences.</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">,</span> <span class="n" style="color: #333;">raw_iterator</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="LC282" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_iterator</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC285" 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="LC286" class="line" lang="python"> <span class="n" style="color: #333;">seq</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="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__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="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">">"</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">descr</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC292" 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="LC293" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">descr</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_fasta_header_line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span> <span class="n" style="color: #333;">line</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</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="LC298" class="line" lang="python"> <span class="n" style="color: #333;">descr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">seq</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="p">,</span> <span class="s" style="color: #d14;">"FASTA file does not start with '>'."</span></span>
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<pre style="margin: 0;">-<span id="LC302" 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;">line</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="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</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="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span><span class="p">:</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">descr</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC306" 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="LC307" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">descr</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_sequence_lengths</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="LC312" class="line" lang="python"> <span class="n" style="color: #333;">seqname</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="LC313" class="line" lang="python"> <span class="n" style="color: #333;">seqlengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__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="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">">"</span> <span class="p">):</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqname</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="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">seqlengths</span><span class="p">[</span> <span class="n" style="color: #333;">seqname</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_fasta_header_line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span> <span class="n" style="color: #333;">line</span> <span class="p">)</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">seqname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">seqname</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="p">,</span> <span class="s" style="color: #d14;">"FASTA file does not start with '>'."</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">length</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;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqname</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="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">seqlengths</span><span class="p">[</span> <span class="n" style="color: #333;">seqname</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seqlengths</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> </span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="nd">@staticmethod</span> </span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_import_pysam</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">pysam</span></span>
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<pre style="margin: 0;">-<span id="LC331" 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="LC332" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"Please install the 'pysam' package to be able to use the Fasta indexing functionality."</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">build_index</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">force</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="LC338" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_import_pysam</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC339" 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;">isinstance</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;">fos</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">,</span> <span class="s" style="color: #d14;">"This function only works with FastaReader objects "</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="s" style="color: #d14;">"connected to a fasta file via file name"</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">index_filename</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;">fos</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fai"</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span> <span class="n" style="color: #333;">index_filename</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">R_OK</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">force</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stat</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;">filename_or_sequence</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">st_mtime</span> <span class="o" style="font-weight: 600;"><=</span> \</span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span> <span class="n" style="color: #333;">index_filename</span> <span class="p">)</span><span class="o" style="font-weight: 600;">.</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="LC346" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># index is up to date</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</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;">fos</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC349" 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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span> <span class="n" style="color: #333;">index_filename</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">R_OK</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Building of Fasta index failed due to unknown error."</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC353" 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;">isinstance</span><span class="p">(</span> <span class="n" style="color: #333;">iv</span><span class="p">,</span> <span class="n" style="color: #333;">GenomicInterval</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">,</span> <span class="s" style="color: #d14;">"GenomicInterval expected as key."</span></span>
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<pre style="margin: 0;">-<span id="LC355" 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;">isinstance</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;">fos</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">,</span> <span class="s" style="color: #d14;">"This function only works with FastaReader objects "</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="s" style="color: #d14;">"connected to a fasta file via file name"</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_import_pysam</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</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;">fos</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">ans</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">(</span> <span class="n" style="color: #333;">fasta</span> <span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC361" 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;">ans</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">ans</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">iv</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</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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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ans</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="LC365" 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="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ans</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_reverse_complement</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqReader</span><span class="p">(</span> <span class="n" style="color: #333;">FileOrSequence</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="s" style="color: #d14;">"""A Fastq object is associated with a FASTQ self.file. When an iterator</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"><span class="s" style="color: #d14;"> is requested from the object, the FASTQ file is read.</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"><span class="s" style="color: #d14;"> </span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"><span class="s" style="color: #d14;"> qual_scale is one of "phred", "solexa", "solexa-old".</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">FileOrSequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="s" style="color: #d14;">"""A Fasta_Reader is associated with a FASTA file or an open connection</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"><span class="s" style="color: #d14;"> to a file-like object with content in FASTA format.</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> It can generate an iterator over the sequences.</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">,</span> <span class="n" style="color: #333;">qual_scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"phred"</span><span class="p">,</span> <span class="n" style="color: #333;">raw_iterator</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="LC376" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual_scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual_scale</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qual_scale</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span> <span class="s" style="color: #d14;">"phred"</span><span class="p">,</span> <span class="s" style="color: #d14;">"solexa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"solexa-old"</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Illegal quality scale."</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_iterator</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC382" 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="LC383" class="line" lang="python"> <span class="n" style="color: #333;">fin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__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="LC384" 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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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC386" 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;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qual</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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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">id1</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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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span> <span class="s" style="color: #d14;">"Number of lines in FASTQ file is not "</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="s" style="color: #d14;">"a multiple of 4. Discarding the last, "</span></span>
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python"> <span class="s" style="color: #d14;">"incomplete record"</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> </span>
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396
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<pre style="margin: 0;">-<span id="LC396" 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;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="p">):</span></span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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398
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<pre style="margin: 0;">-<span id="LC398" 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;">id1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"@"</span> <span class="p">):</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span> <span class="s" style="color: #d14;">"Primary ID line in FASTQ file does"</span></span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="s" style="color: #d14;">"not start with '@'. Either this is not FASTQ data or the parser got out of sync."</span> <span class="p">)</span></span>
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401
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<pre style="margin: 0;">-<span id="LC401" 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;">id2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"+"</span> <span class="p">):</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span> <span class="s" style="color: #d14;">"Secondary ID line in FASTQ file does"</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"> <span class="s" style="color: #d14;">"not start with '+'. Maybe got out of sync."</span> <span class="p">)</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="n" style="color: #333;">id2</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">id1</span><span class="p">[</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;">id2</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="LC405" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span> <span class="s" style="color: #d14;">"Primary and secondary ID line in FASTQ"</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="s" style="color: #d14;">"disagree."</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</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;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq</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 class="n" style="color: #333;">id1</span><span class="p">[</span><span class="mi" style="color: #099;">1</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 class="n" style="color: #333;">qual</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 class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual_scale</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="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SequenceWithQualities</span><span class="p">(</span> <span class="n" style="color: #333;">seq</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 class="n" style="color: #333;">id1</span><span class="p">[</span><span class="mi" style="color: #099;">1</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 class="n" style="color: #333;">qual</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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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual_scale</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BowtieReader</span><span class="p">(</span> <span class="n" style="color: #333;">FileOrSequence</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="s" style="color: #d14;">"""A BowtieFile object is associated with a Bowtie output file that </span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"><span class="s" style="color: #d14;"> contains short read alignments. It can generate an iterator of Alignment</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"><span class="s" style="color: #d14;"> objects."""</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC420" 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="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__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="LC422" 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="LC423" class="line" lang="python"> <span class="n" style="color: #333;">algnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BowtieAlignment</span><span class="p">(</span> <span class="n" style="color: #333;">line</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"Reported "</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span> <span class="s" style="color: #d14;">"BowtieReader: Ignoring the following line, which could not be parsed:</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">line</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="nb" style="color: #0086b3;">RuntimeWarning</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">algnt</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bundle_multiple_alignments</span><span class="p">(</span> <span class="n" style="color: #333;">sequence_of_alignments</span> <span class="p">):</span> </span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">,</span> <span class="n" style="color: #333;">raw_iterator</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="LC285" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_iterator</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" 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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<td class="diff-line-num new new_line" data-linenumber="289" 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">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" 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">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="293" 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">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">descr</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="295" 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">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">descr</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">s</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_fasta_header_line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</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 new new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">descr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="304" 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">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">seq</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="p">,</span> <span class="s" style="color: #d14;">"FASTA file does not start with '>'."</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" 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;">line</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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<td class="diff-line-num new new_line" data-linenumber="306" 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">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</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="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="307" 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">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span><span class="p">:</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">descr</span><span class="p">)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">descr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">descr</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">s</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_sequence_lengths</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">seqname</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">seqlengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">):</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqname</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="p">:</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">seqlengths</span><span class="p">[</span> <span class="n" style="color: #333;">seqname</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_fasta_header_line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">seqname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="325" 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">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">seqname</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="p">,</span> <span class="s" style="color: #d14;">"FASTA file does not start with '>'."</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">length</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;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">())</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqname</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="p">:</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">seqlengths</span><span class="p">[</span> <span class="n" style="color: #333;">seqname</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seqlengths</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"> <span class="nd">@staticmethod</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_import_pysam</span><span class="p">():</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">pysam</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" 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="LC335" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Please install the 'pysam' package to be able to use the Fasta indexing functionality."</span><span class="p">)</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">build_index</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">force</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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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_import_pysam</span><span class="p">()</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" 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;">isinstance</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;">fos</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">,</span> <span class="s" style="color: #d14;">"This function only works with FastaReader objects "</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="s" style="color: #d14;">"connected to a fasta file via file name"</span></span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">index_filename</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;">fos</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fai"</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span><span class="n" style="color: #333;">index_filename</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">R_OK</span><span class="p">):</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">force</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stat</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;">filename_or_sequence</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">st_mtime</span> <span class="o" style="font-weight: 600;"><=</span> \</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">index_filename</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">st_mtime</span><span class="p">:</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># index is up to date</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</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;">fos</span><span class="p">)</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" 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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">access</span><span class="p">(</span><span class="n" style="color: #333;">index_filename</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">R_OK</span><span class="p">):</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Building of Fasta index failed due to unknown error."</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="p">):</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" 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;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">iv</span><span class="p">,</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">):</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">,</span> <span class="s" style="color: #d14;">"GenomicInterval expected as key."</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" 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;">isinstance</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;">fos</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">,</span> <span class="s" style="color: #d14;">"This function only works with FastaReader objects "</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="s" style="color: #d14;">"connected to a fasta file via file name"</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_import_pysam</span><span class="p">()</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">faidx</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;">fos</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</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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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">ans</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">))</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" 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;">ans</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">ans</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">iv</span><span class="p">)</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</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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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ans</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" 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="LC369" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ans</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_reverse_complement</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FastqReader</span><span class="p">(</span><span class="n" style="color: #333;">FileOrSequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="s" style="color: #d14;">"""A Fastq object is associated with a FASTQ self.file. When an iterator</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"><span class="s" style="color: #d14;"> is requested from the object, the FASTQ file is read.</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="s" style="color: #d14;"> qual_scale is one of "phred", "solexa", "solexa-old".</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">,</span> <span class="n" style="color: #333;">qual_scale</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"phred"</span><span class="p">,</span> <span class="n" style="color: #333;">raw_iterator</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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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file_</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual_scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual_scale</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qual_scale</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"phred"</span><span class="p">,</span> <span class="s" style="color: #d14;">"solexa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"solexa-old"</span><span class="p">):</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Illegal quality scale."</span><span class="p">)</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">raw_iterator</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC386" 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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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">fin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" 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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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" 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;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fin</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qual</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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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">id1</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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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"> <span class="s" style="color: #d14;">"Number of lines in FASTQ file is not "</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"> <span class="s" style="color: #d14;">"a multiple of 4. Discarding the last, "</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"> <span class="s" style="color: #d14;">"incomplete record"</span><span class="p">)</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"></span>
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401
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<pre style="margin: 0;">+<span id="LC401" 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;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">):</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" 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;">id1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"@"</span><span class="p">):</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Primary ID line in FASTQ file does"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="405" 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">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="s" style="color: #d14;">"not start with '@'. Either this is not FASTQ data or the parser got out of sync."</span><span class="p">)</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" 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;">id2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"+"</span><span class="p">):</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Secondary ID line in FASTQ file does"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="s" style="color: #d14;">"not start with '+'. Maybe got out of sync."</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="409" 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">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">id2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">id1</span><span class="p">[</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;">id2</span><span class="p">[</span><span class="mi" style="color: #099;">1</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="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Primary and secondary ID line in FASTQ"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="s" style="color: #d14;">"disagree."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raw_iterator</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq</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 class="n" style="color: #333;">id1</span><span class="p">[</span><span class="mi" style="color: #099;">1</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 class="n" style="color: #333;">qual</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 class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual_scale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC415" 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="LC416" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SequenceWithQualities</span><span class="p">(</span><span class="n" style="color: #333;">seq</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 class="n" style="color: #333;">id1</span><span class="p">[</span><span class="mi" style="color: #099;">1</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 class="n" style="color: #333;">qual</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="LC417" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual_scale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BowtieReader</span><span class="p">(</span><span class="n" style="color: #333;">FileOrSequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="s" style="color: #d14;">"""A BowtieFile object is associated with a Bowtie output file that</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"><span class="s" style="color: #d14;"> contains short read alignments. It can generate an iterator of Alignment</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"><span class="s" style="color: #d14;"> objects."""</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="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="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__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="LC428" 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="LC429" class="line" lang="python"> <span class="n" style="color: #333;">algnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BowtieAlignment</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"Reported "</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"BowtieReader: Ignoring the following line, which could not be parsed:</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">line</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"> <span class="nb" style="color: #0086b3;">RuntimeWarning</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">algnt</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bundle_multiple_alignments</span><span class="p">(</span><span class="n" style="color: #333;">sequence_of_alignments</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"> <span class="s" style="color: #d14;">"""Some alignment programs, e.g., Bowtie, can output multiple alignments,</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"><span class="s" style="color: #d14;"> i.e., the same read is reported consecutively with different alignments.</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"><span class="s" style="color: #d14;"> This function takes an iterator over alignments and bundles consecutive</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"><span class="s" style="color: #d14;"> alignments regarding the same read to a list of Alignment objects and</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"><span class="s" style="color: #d14;"> returns an iterator over these.</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">alignment_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">sequence_of_alignments</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">alignment_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">sequence_of_alignments</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python"> <span class="n" style="color: #333;">algnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_iter</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python"> <span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="n" style="color: #333;">algnt</span> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">algnt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignment_iter</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">@@ -443,75 +450,75 @@ def bundle_multiple_alignments( sequence_of_alignments ):</td>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">ma</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">ma</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="n" style="color: #333;">algnt</span> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC452" 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="LC446" class="line" lang="python"> <span class="n" style="color: #333;">ma</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">algnt</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">ma</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SolexaExportAlignment</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">Alignment</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">ma</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">algnt</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">ma</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SolexaExportAlignment</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Alignment</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="s" style="color: #d14;">"""Iterating over SolexaExportReader objects will yield SoelxaExportRecord</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"><span class="s" style="color: #d14;"> objects. These have four fields:</span></span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="python"><span class="s" style="color: #d14;"> read - a SequenceWithQualities object<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"><span class="s" style="color: #d14;"> read - a SequenceWithQualities object</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"><span class="s" style="color: #d14;"> aligned - a boolean, indicating whether the object was aligned</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"><span class="s" style="color: #d14;"> iv - a GenomicInterval giving the alignment (or None, if not aligned)</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"><span class="s" style="color: #d14;"> passed_filter - a boolean, indicating whether the object passed the filter</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"><span class="s" style="color: #d14;"> nomatch_code - a code indicating why no match was found (or None, if the</span></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"><span class="s" style="color: #d14;"> read was aligned)</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="python"><span class="s" style="color: #d14;"> As long as 'aligned' is True, a SolexaExportRecord can be treated as an<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"><span class="s" style="color: #d14;"> As long as 'aligned' is True, a SolexaExportRecord can be treated as an</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"><span class="s" style="color: #d14;"> Alignment object.</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Data is filled in by SolexaExportRecord</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"< </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s object: Read '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s', aligned to </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</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;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</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;">iv</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</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;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</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;">iv</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC479" 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="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"< </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s object: Non-aligned read '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</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;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"< </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s object: Non-aligned read '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</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;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SolexaExportReader</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">FileOrSequence</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SolexaExportReader</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">FileOrSequence</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parser for *_export.txt files from the SolexaPipeline software.</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"><span class="s" style="color: #d14;"> Iterating over a SolexaExportReader yields SolexaExportRecord objects.</span></span>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">solexa_old</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">solexa_old</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">solexa_old</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualscale</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"solexa-old"</span></span>
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<pre style="margin: 0;"> <span id="LC493" 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="LC494" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualscale</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"solexa"</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_line_bare</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">dummy</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_line_bare</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">dummy</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</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 class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</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="LC500" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="python"> <span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'machine'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'run_number'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'lane'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'tile'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'x_coord'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'y_coord'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'index_string'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'read_nbr'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'read_seq'</span><span class="p">],</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'qual_str'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'chrom'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'contig'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'pos'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'strand'</span><span class="p">],</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'match_descr'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'single_read_algnt_score'</span><span class="p">],</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'paired_read_algnt_score'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_chrom'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_contig'</span><span class="p">],</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_offset'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_strand'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'passed_filtering'</span><span class="p">]</span><span class="idiff left right"> </span><span class="p">)</span> \</span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'machine'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'run_number'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'lane'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'tile'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'x_coord'</span></span><span class="p"><span class="idiff right">],</span></span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'y_coord'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'index_string'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'read_nbr'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'read_seq'</span><span class="p">],</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'qual_str'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'chrom'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'contig'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'pos'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'strand'</span><span class="p">],</span></span>
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<td class="diff-line-num new new_line" data-linenumber="504" 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="LC504" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'match_descr'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'single_read_algnt_score'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'paired_read_algnt_score'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_chrom'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_contig'</span><span class="p">],</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_offset'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'partner_strand'</span><span class="p">],</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="s" style="color: #d14;">'passed_filtering'</span><span class="p">])</span> \</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC503" 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="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff"> </span><span class="p"><span class="idiff">):</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC510" 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;"><span class="idiff left">self</span></span><span class="p"><span class="idiff right">):</span></span></span>
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python"> <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SolexaExportAlignment</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC506" 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;">SolexaExportReader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_line_bare</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC513" 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;">SolexaExportReader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_line_bare</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">line</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'read_nbr'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="idiff left right"> </span><span class="s" style="color: #d14;">"Paired-end read encountered. PE is so far supported only for "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="python"> <span class="s" style="color: #d14;">"SAM files, not yet for SolexaExport. All PE-related fields are ignored. "</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SequenceWithQualities</span><span class="p">(</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="python"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'read_seq'</span><span class="p">],</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s#0"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'machine'</span><span class="p">],</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'lane'</span><span class="p">],</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'tile'</span><span class="p">],</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'x_coord'</span><span class="p">],</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'y_coord'</span><span class="p">]</span><span class="idiff left right"> </span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'qual_str'</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;">qualscale</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Paired-end read encountered. PE is so far supported only for "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="s" style="color: #d14;">"SAM files, not yet for SolexaExport. All PE-related fields are ignored. "</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SequenceWithQualities</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'read_seq'</span><span class="p">],</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s#0"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'machine'</span><span class="p">],</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'lane'</span><span class="p">],</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'tile'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'x_coord'</span><span class="p">],</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'y_coord'</span><span class="p">]),</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'qual_str'</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;">qualscale</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'passed_filtering'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Y'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">passed_filter</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="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'passed_filtering'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'N'</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="529" 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">@@ -529,115 +536,116 @@ class SolexaExportReader( FileOrSequence ):</td>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span></span>
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<pre style="margin: 0;"> <span id="LC537" 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="LC538" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Illegal strand value in Solexa export data."</span></span>
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'pos'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">start</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;"><span class="idiff left">fields</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'pos'</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="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'chrom'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'chrom'</span><span class="p">]</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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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="s" style="color: #d14;">'contig'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">fields</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'read_seq'</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">strand</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</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"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">start</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;"><span class="idiff left">fields</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'read_seq'</span></span><span class="p"><span class="idiff">]),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">strand</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">record</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SAM_Reader</span><span class="p">(</span> <span class="n" style="color: #333;">FileOrSequence</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"> <span class="s" style="color: #d14;">"""A SAM_Reader object is associated with a SAM file that </span></span>
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python"><span class="s" style="color: #d14;"> contains short read alignments. It can generate an iterator of Alignment</span></span>
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<pre style="margin: 0;">-<span id="LC543" class="line" lang="python"><span class="s" style="color: #d14;"> objects."""</span></span>
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC545" 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="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__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="LC547" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"@"</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># do something with the header line</span></span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC550" 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="LC551" class="line" lang="python"> <span class="n" style="color: #333;">algnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_Alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_SAM_line</span><span class="p">(</span> <span class="n" style="color: #333;">line</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">+</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;">get_line_number_string</span><span class="p">(),</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">algnt</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GenomicArrayOfSets</span><span class="p">(</span> <span class="n" style="color: #333;">GenomicArray</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="s" style="color: #d14;">"""A GenomicArrayOfSets is a specialization of GenomicArray that allows to store</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="python"><span class="s" style="color: #d14;"> sets of objects. On construction, the step vectors are initialized with empty sets.</span></span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="python"><span class="s" style="color: #d14;"> By using the 'add_value' method, objects can be added to intervals. If an object</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="python"><span class="s" style="color: #d14;"> is already present in the set(s) at this interval, an the new object is added to</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="python"><span class="s" style="color: #d14;"> the present set, and the set is split if necessary.</span></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">stranded</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;">storage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'step'</span><span class="p">,</span> <span class="n" style="color: #333;">memmap_dir</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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<pre style="margin: 0;">-<span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">GenomicArray</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">stranded</span><span class="p">,</span> <span class="s" style="color: #d14;">'O'</span><span class="p">,</span> <span class="n" style="color: #333;">storage</span><span class="p">,</span> <span class="n" style="color: #333;">memmap_dir</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_chrom</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maxint</span><span class="p">,</span> <span class="n" style="color: #333;">start_index</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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<pre style="margin: 0;">-<span id="LC570" class="line" lang="python"> <span class="n" style="color: #333;">GenomicArray</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_chrom</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">start_index</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom_vectors</span><span class="p">[</span> <span class="n" style="color: #333;">chrom</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="python"> <span class="n" style="color: #333;">cv</span><span class="p">[:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="python"> <span class="n" style="color: #333;">cv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_vector_of_sets</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="LC574" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SAM_Reader</span><span class="p">(</span><span class="n" style="color: #333;">FileOrSequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="s" style="color: #d14;">"""A SAM_Reader object is associated with a SAM file that</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="python"><span class="s" style="color: #d14;"> contains short read alignments. It can generate an iterator of Alignment</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"><span class="s" style="color: #d14;"> objects."""</span></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC553" 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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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"@"</span><span class="p">):</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># do something with the header line</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="python"> <span class="n" style="color: #333;">algnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SAM_Alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_SAM_line</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="python"> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">+</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;">get_line_number_string</span><span class="p">(),)</span></span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">algnt</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">GenomicArrayOfSets</span><span class="p">(</span><span class="n" style="color: #333;">GenomicArray</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="python"> <span class="s" style="color: #d14;">"""A GenomicArrayOfSets is a specialization of GenomicArray that allows to store</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="python"><span class="s" style="color: #d14;"> sets of objects. On construction, the step vectors are initialized with empty sets.</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"><span class="s" style="color: #d14;"> By using the 'add_value' method, objects can be added to intervals. If an object</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="python"><span class="s" style="color: #d14;"> is already present in the set(s) at this interval, an the new object is added to</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="python"><span class="s" style="color: #d14;"> the present set, and the set is split if necessary.</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">stranded</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;">storage</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'step'</span><span class="p">,</span> <span class="n" style="color: #333;">memmap_dir</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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<pre style="margin: 0;">+<span id="LC575" class="line" lang="python"> <span class="n" style="color: #333;">GenomicArray</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chroms</span><span class="p">,</span> <span class="n" style="color: #333;">stranded</span><span class="p">,</span> <span class="s" style="color: #d14;">'O'</span><span class="p">,</span> <span class="n" style="color: #333;">storage</span><span class="p">,</span> <span class="n" style="color: #333;">memmap_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_chrom</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maxint</span><span class="p">,</span> <span class="n" style="color: #333;">start_index</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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<pre style="margin: 0;">+<span id="LC578" class="line" lang="python"> <span class="n" style="color: #333;">GenomicArray</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_chrom</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">start_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom_vectors</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"> <span class="n" style="color: #333;">cv</span><span class="p">[:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="python"> <span class="n" style="color: #333;">cv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_vector_of_sets</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="LC582" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">###########################</span></span>
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">## paired-end handling</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">###########################</span></span>
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pair_SAM_alignments</span><span class="p">(</span> <span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">bundle</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="LC582" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="python"> <span class="n" style="color: #333;">mate_missing_count</span> <span class="o" style="font-weight: 600;">=</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="LC584" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC585" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_list</span><span class="p">(</span> <span class="n" style="color: #333;">almnt_list</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="n" style="color: #333;">almnt_list</span> <span class="p">)</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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<pre style="margin: 0;">-<span id="LC587" class="line" lang="python"> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">almnt_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</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="LC588" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Find its mate</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">almnt_list</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span><span class="p">:</span></span>
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591
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span><span class="p">):</span></span>
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595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC599" 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="LC600" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">mate_missing_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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602
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mate_missing_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="LC603" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span> <span class="s" style="color: #d14;">"Read "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" claims to have an aligned mate "</span> <span class="o" style="font-weight: 600;">+</span></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"> <span class="s" style="color: #d14;">"which could not be found in an adjacent line."</span> <span class="p">)</span></span>
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605
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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606
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a2</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="p">:</span></span>
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607
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span> <span class="n" style="color: #333;">a2</span> <span class="p">)</span></span>
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608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"first"</span><span class="p">:</span></span>
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609
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span> <span class="n" style="color: #333;">a1</span><span class="p">,</span> <span class="n" style="color: #333;">a2</span> <span class="p">)</span></span>
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610
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"second"</span></span>
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612
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span> <span class="n" style="color: #333;">a2</span><span class="p">,</span> <span class="n" style="color: #333;">a1</span> <span class="p">)</span></span>
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613
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python"></span>
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614
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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615
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python"> <span class="n" style="color: #333;">current_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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616
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">almnt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignments</span><span class="p">:</span></span>
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617
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<pre style="margin: 0;">-<span id="LC617" 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;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired_end</span><span class="p">:</span></span>
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618
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"'pair_alignments' needs a sequence of paired-end alignments"</span></span>
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619
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<pre style="margin: 0;">-<span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">:</span></span>
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620
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<pre style="margin: 0;">-<span id="LC620" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Paired-end read found with 'unknown' 'pe_which' status."</span></span>
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621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">current_name</span><span class="p">:</span></span>
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622
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">almnt</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC623" 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="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bundle</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span> <span class="n" style="color: #333;">process_list</span><span class="p">(</span> <span class="n" style="color: #333;">almnt_list</span> <span class="p">)</span> <span class="p">)</span></span>
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626
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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627
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">process_list</span><span class="p">(</span> <span class="n" style="color: #333;">almnt_list</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">p</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="python"> <span class="n" style="color: #333;">current_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="n" style="color: #333;">almnt</span> <span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bundle</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span> <span class="n" style="color: #333;">process_list</span><span class="p">(</span> <span class="n" style="color: #333;">almnt_list</span> <span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC633" 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="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">process_list</span><span class="p">(</span> <span class="n" style="color: #333;">almnt_list</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">p</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mate_missing_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="LC637" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d reads with missing mate encountered."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">mate_missing_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pair_SAM_alignments</span><span class="p">(</span><span class="n" style="color: #333;">alignments</span><span class="p">,</span> <span class="n" style="color: #333;">bundle</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="LC590" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"> <span class="n" style="color: #333;">mate_missing_count</span> <span class="o" style="font-weight: 600;">=</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="LC592" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_list</span><span class="p">(</span><span class="n" style="color: #333;">almnt_list</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">almnt_list</span><span class="p">)</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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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">almnt_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</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="LC596" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># Find its mate</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">almnt_list</span><span class="p">:</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span><span class="p">:</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span><span class="p">:</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span><span class="p">):</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">a2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span><span class="p">:</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span><span class="p">:</span></span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">mate_missing_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mate_missing_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</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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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Read "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" claims to have an aligned mate "</span> <span class="o" style="font-weight: 600;">+</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="s" style="color: #d14;">"which could not be found in an adjacent line."</span><span class="p">)</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">a2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a2</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="p">:</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">a2</span><span class="p">)</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"first"</span><span class="p">:</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">a1</span><span class="p">,</span> <span class="n" style="color: #333;">a2</span><span class="p">)</span></span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"second"</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">a2</span><span class="p">,</span> <span class="n" style="color: #333;">a1</span><span class="p">)</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="python"></span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">current_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">almnt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignments</span><span class="p">:</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" 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;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired_end</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="626" 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">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"'pair_alignments' needs a sequence of paired-end alignments"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="627" 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">
627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="628" 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">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Paired-end read found with 'unknown' 'pe_which' status."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="629" 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">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">current_name</span><span class="p">:</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">almnt</span><span class="p">)</span></span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bundle</span><span class="p">:</span></span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">process_list</span><span class="p">(</span><span class="n" style="color: #333;">almnt_list</span><span class="p">))</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="635" 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">
635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">process_list</span><span class="p">(</span><span class="n" style="color: #333;">almnt_list</span><span class="p">):</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">p</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="python"> <span class="n" style="color: #333;">current_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="python"> <span class="n" style="color: #333;">almnt_list</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">almnt</span><span class="p">]</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bundle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">process_list</span><span class="p">(</span><span class="n" style="color: #333;">almnt_list</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC641" 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="LC642" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">process_list</span><span class="p">(</span><span class="n" style="color: #333;">almnt_list</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">p</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mate_missing_count</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="LC645" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d reads with missing mate encountered."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">mate_missing_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="LC646" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC640" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pair_SAM_alignments_with_buffer</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">alignments</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_buffer_size</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">30000000</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pair_SAM_alignments_with_buffer</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">alignments</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">max_buffer_size</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">30000000</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"> <span class="n" style="color: #333;">almnt_buffer</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python"> <span class="n" style="color: #333;">ambiguous_pairing_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</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">@@ -648,56 +656,56 @@ def pair_SAM_alignments_with_buffer( alignments, max_buffer_size=30000000 ):</td>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Cannot process paired-end alignment found with 'unknown' 'pe_which' status."</span></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python"> <span class="n" style="color: #333;">matekey</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"> <span class="n" style="color: #333;">matekey</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="python"> <span class="s" style="color: #d14;">"second"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"first"</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"first"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inferred_insert_size</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inferred_insert_size</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python"></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;">matekey</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">almnt_buffer</span></span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matekey</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </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="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">almnt_buffer</span></span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">matekey</span></span><span class="idiff"> </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="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python"> <span class="n" style="color: #333;">mate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">[</span> <span class="n" style="color: #333;">matekey</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="LC671" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">[</span> <span class="n" style="color: #333;">matekey</span> <span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC672" 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="LC665" class="line" lang="python"> <span class="n" style="color: #333;">mate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">[</span> <span class="n" style="color: #333;">matekey</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="idiff left"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="python"> <span class="n" style="color: #333;">mate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">[</span> <span class="n" style="color: #333;">matekey</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC674" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ambiguous_pairing_counter</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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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">ambiguous_pairing_first_occurance</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matekey</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">ambiguous_pairing_counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"first"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">almnt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mate</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">almnt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mate</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC679" 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="LC672" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">mate</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">almnt</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">mate</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">almnt</span></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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<pre style="margin: 0;">-<span id="LC674" class="line" lang="python"> <span class="n" style="color: #333;">almntkey</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inferred_insert_size</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">almntkey</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_start</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python"> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inferred_insert_size</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aligned</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_aligned</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almntkey</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python"> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">[</span> <span class="n" style="color: #333;">almntkey</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="n" style="color: #333;">almnt</span> <span class="p">]</span></span>
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683
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<pre style="margin: 0;"> <span id="LC691" 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="LC684" class="line" lang="python"> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">[</span> <span class="n" style="color: #333;">almntkey</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">almnt</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">almnt_buffer</span><span class="p">[</span> <span class="n" style="color: #333;">almntkey</span> <span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">almnt</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">almnt_buffer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_buffer_size</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maximum alignment buffer size exceeded while pairing SAM alignments."</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">almnt_buffer</span><span class="p">)</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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<pre style="margin: 0;">-<span id="LC689" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"Mate records missing for </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d records; first such record: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s."</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="python"> <span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">almnt_buffer</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">almnt_buffer</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">values</span></span><span class="p"><span class="idiff">()[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"Mate records missing for </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">d records; first such record: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s."</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python"> <span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">almnt_buffer</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">almnt_buffer</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">values</span></span><span class="p"><span class="idiff">()[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]))</span>)</span></span>
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691
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">almnt_list</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">almnt_buffer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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692
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700
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">almnt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">almnt_list</span><span class="p">:</span></span>
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693
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701
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">almnt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pe_which</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"first"</span><span class="p">:</span></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">almnt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">almnt</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">)</span></span>
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695
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">almnt</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</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"> </span><span class="n" style="color: #333;"><span class="idiff right">almnt</span></span><span class="p">)</span></span>
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697
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"></span>
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698
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ambiguous_pairing_counter</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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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="idiff left right"> </span><span class="s" style="color: #d14;">"Mate pairing was ambiguous for </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d records; mate key for first such record: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s."</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="python"> <span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ambiguous_pairing_counter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ambiguous_pairing_first_occurance</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Mate pairing was ambiguous for </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d records; mate key for first such record: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s."</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">ambiguous_pairing_counter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ambiguous_pairing_first_occurance</span></span><span class="p"><span class="idiff right">))</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"></span>
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702
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">###########################</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">@@ -705,11 +713,11 @@ def pair_SAM_alignments_with_buffer( alignments, max_buffer_size=30000000 ):</td>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">###########################</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="python"><span class="n" style="color: #333;">_re_vcf_meta_comment</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="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"^##([a-zA-Z]+)</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s" style="color: #d14;"><span class="idiff">=(.*)$"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="python"><span class="n" style="color: #333;">_re_vcf_meta_comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"^##([a-zA-Z]+)</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s" style="color: #d14;"><span class="idiff right">=(.*)$"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"><span class="n" style="color: #333;">_re_vcf_meta_descr</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;">'ID=[^,]+,?|Number=[^,]+,?|Type=[^,]+,?|Description="[^"]+",?'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="python"><span class="n" style="color: #333;">_re_vcf_meta_types</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="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"[INFO|FILTER|FORMAT]"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"><span class="n" style="color: #333;">_re_vcf_meta_types</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;"><span class="idiff left right">"[INFO|FILTER|FORMAT]"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"><span class="n" style="color: #333;">_vcf_typemap</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"> <span class="s" style="color: #d14;">"Integer"</span><span class="p">:</span><span class="nb" style="color: #0086b3;">int</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">@@ -718,9 +726,9 @@ _vcf_typemap = {</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"> <span class="s" style="color: #d14;">"Flag"</span><span class="p">:</span><span class="nb" style="color: #0086b3;">bool</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VariantCall</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">object</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">identifier</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filtr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VariantCall</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">object</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">identifier</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filtr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </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="LC732" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chrom</span></span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span></span>
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">identifier</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">@@ -730,9 +738,9 @@ class VariantCall( object ):</td>
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filtr</span></span>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_original_line</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="LC733" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC735" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fromdict</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cls</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">dictionary</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fromdict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">cls</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dictionary</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dictionary</span><span class="p">[</span><span class="s" style="color: #d14;">"chrom"</span><span class="p">]</span></span>
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dictionary</span><span class="p">[</span><span class="s" style="color: #d14;">"pos"</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">@@ -745,7 +753,7 @@ class VariantCall( object ):</td>
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_original_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="python"></span>
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fromline</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">cls</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nsamples</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sampleids</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="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fromline</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">cls</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nsamples</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sampleids</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 right">[]</span>):</span></span>
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="p">()</span></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nsamples</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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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</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">@@ -757,106 +765,106 @@ class VariantCall( object ):</td>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="python"> <span class="n" style="color: #333;">spos</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">9</span></span>
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sampleids</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="p">[</span> <span class="n" style="color: #333;">sid</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">itertools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">format</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lsplit</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">spos</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">":"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="p">[</span> <span class="n" style="color: #333;">sid</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">itertools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">format</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lsplit</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">spos</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">":"</span></span><span class="p"><span class="idiff right">))</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"> <span class="n" style="color: #333;">spos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicPosition</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicPosition</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">alt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">alt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_original_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">infoline</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">infoline</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">";"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">((</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">key</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</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;">info</span><span class="p">[</span><span class="n" style="color: #333;">key</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;">info</span><span class="idiff left right"> </span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">";"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">((</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">key</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"="</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</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;">info</span><span class="p">[</span><span class="n" style="color: #333;">key</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;">info</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC778" 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="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span></span>
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_original_line</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"Original line is empty, probably this object was created from scratch and not from a line in a .vcf file!"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_original_line</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"Original line is empty, probably this object was created from scratch and not from a line in a .vcf file!"</span></span><span class="p">)</span></span>
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775
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783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_original_line</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="python"><span class="idiff left right"> </span></span>
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777
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sampleline</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python"></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sampleline</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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778
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</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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779
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"No samples in this variant call!"</span><span class="idiff left right"> </span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"No samples in this variant call!"</span></span>
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780
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span></span>
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781
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"> <span class="n" style="color: #333;">keys</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;">format</span></span>
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782
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">keys</span></span><span class="p">)</span> <span class="p">]</span></span>
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783
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sid</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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784
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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785
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793
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">:</span></span>
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786
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">samples</span><span class="p">[</span><span class="n" style="color: #333;">sid</span><span class="p">]:</span></span>
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787
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">samples</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">sid</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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788
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">":"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC790" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_line</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">samples</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">sid</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff right">]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python"> <span class="n" style="color: #333;">ret</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">":"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ret</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_line</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</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="LC793" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">infoline</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">infoline</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">])</span>)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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794
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<pre style="margin: 0;"> <span id="LC802" 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="LC795" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">infoline</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sampleline</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__descr__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">id</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ref</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">alt</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">qual</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">infoline</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sampleline</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">])</span>)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python"></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__descr__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<VariantCall at </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, ref '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s', alt </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</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;">pos</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"/."</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;">ref</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</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;">alt</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"[]"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC799" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="python"></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s:'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'-></span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</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;">pos</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"/."</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;">ref</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</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;">alt</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">"[]"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unpack_info</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">infodict</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">unpack_info</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">infodict</span></span><span class="p">):</span></span>
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804
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">token</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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;">"="</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"> <span class="n" style="color: #333;">token</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span></span>
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808
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">infodict</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_key</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">token</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">infodict</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">infodict</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_key</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">token</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">infodict</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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810
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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811
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">token</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">token</span><span class="p">[</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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812
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">tmp</span></span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff right"> </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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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">tmp</span></span><span class="p"><span class="idiff">[</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">token</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">]</span>)</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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813
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821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">token</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">token</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="LC822" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;">#Flag attribute found</span></span>
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">token</span><span class="p">]</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="LC816" class="line" lang="python"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">infodict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">difference</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">set</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="python"> <span class="n" style="color: #333;">diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">infodict</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff">())</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">difference</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">())</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">diff</span><span class="p">:</span></span>
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826
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">infodict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">:</span></span>
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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820
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span></span>
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC822" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VCF_Reader</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">FileOrSequence</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VCF_Reader</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">FileOrSequence</span></span><span class="p">):</span></span>
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC824" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename_or_sequence</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename_or_sequence</span></span><span class="p">)</span></span>
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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827
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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828
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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829
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">formats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nsamples</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="LC839" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sampleids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_info_dict</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">infodict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_vcf_typemap</span></span><span class="p"><span class="idiff">[</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff">][</span></span><span class="s" style="color: #d14;"><span class="idiff">"Type"</span></span><span class="p"><span class="idiff">]]</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_meta</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_info_dict</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">infodict</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_vcf_typemap</span></span><span class="p"><span class="idiff">[</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff">][</span></span><span class="s" style="color: #d14;"><span class="idiff">"Type"</span></span><span class="p"><span class="idiff">]])</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_meta</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">):</span></span>
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837
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header_filename</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="LC838" class="line" lang="python"> <span class="n" style="color: #333;">the_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="python"> <span class="n" style="color: #333;">the_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC847" 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="LC840" class="line" lang="python"> <span class="n" style="color: #333;">the_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"r"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python"> <span class="n" style="color: #333;">the_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">header_filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"r"</span></span><span class="p">)</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="python"></span>
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842
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the_iter</span><span class="p">:</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;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'#'</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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844
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">"##"</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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845
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_vcf_meta_comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'#'</span></span><span class="p">):</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"##"</span></span><span class="p">):</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">mo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_re_vcf_meta_comment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">line</span></span><span class="p">)</span></span>
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846
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mo</span><span class="p">:</span></span>
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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848
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"INFO"</span><span class="p">:</span></span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"="</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_re_vcf_meta_descr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">findall</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"="</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_re_vcf_meta_descr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">findall</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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850
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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851
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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852
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">[</span> <span class="n" style="color: #333;">key</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"FILTER"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"="</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_re_vcf_meta_descr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">findall</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"="</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_re_vcf_meta_descr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">findall</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filters</span><span class="p">[</span> <span class="n" style="color: #333;">key</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"FORMAT"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"="</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_re_vcf_meta_descr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">findall</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">e</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">","</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"="</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_re_vcf_meta_descr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">findall</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">value</span><span class="p">[</span><span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">formats</span><span class="p">[</span> <span class="n" style="color: #333;">key</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</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">@@ -864,51 +872,51 @@ class VCF_Reader( FileOrSequence ):</td>
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">metadata</span><span class="p">[</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC873" 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="LC874" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sampleids</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</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="mi" style="color: #099;">9</span><span class="p">:]</span></span>
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nsamples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sampleids</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nsamples</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;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">sampleids</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC877" 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="LC878" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC871" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">meta_info</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="python"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">==</span></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">the_iter</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">FileOrSequence</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC876" 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="LC877" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">the_iter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"r"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the_iter</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startswith</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'#'</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC882" 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="LC883" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="python"><span class="idiff left right"> </span></span>
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886
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<pre style="margin: 0;">-<span id="LC886" 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="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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887
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<pre style="margin: 0;">-<span id="LC887" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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888
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'#'</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="python"></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">meta_info</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</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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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">is</span></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">the_iter</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">FileOrSequence</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff right">self</span></span><span class="p">)</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">the_iter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">header_filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"r"</span></span><span class="p">)</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="python"></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the_iter</span><span class="p">:</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startswith</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">'#'</span></span><span class="p">):</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">ret</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">append</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">)</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">break</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC894" 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;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'#'</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="python"> <span class="n" style="color: #333;">vc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VariantCall</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fromline</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nsamples</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sampleids</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="python"> <span class="n" style="color: #333;">vc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VariantCall</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fromline</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">line</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nsamples</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">sampleids</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">vc</span></span>
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC894" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">WiggleReader</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">FileOrSequence</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">WiggleReader</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">FileOrSequence</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC896" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">verbose</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename_or_sequence</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">verbose</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename_or_sequence</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stepType</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'none'</span></span>
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">verbose</span></span>
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<pre style="margin: 0;">-<span id="LC901" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC902" 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="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="python"></span>
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910
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<pre style="margin: 0;">+<span id="LC910" 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;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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903
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="python"> <span class="n" style="color: #333;">span</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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913
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<pre style="margin: 0;"> <span id="LC913" class="line" lang="python"> <span class="n" style="color: #333;">step</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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906
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914
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="python"> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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907
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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908
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<pre style="margin: 0;">-<span id="LC908" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'track'</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'track'</span></span><span class="p">):</span></span>
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917
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<pre style="margin: 0;"> <span id="LC917" 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;">shlex</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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910
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918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attributes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">p</span><span class="p">[</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;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">]])</span></span>
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911
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'fixedStep'</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">):</span></span> <span class="c" style="color: #998; font-style: italic;"># do fixed step stuff</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">'fixedStep'</span></span><span class="p"><span class="idiff">):</span></span><span class="idiff right"> </span> <span class="c" style="color: #998; font-style: italic;"># do fixed step stuff</span></span>
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<pre style="margin: 0;"> <span id="LC920" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stepType</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'fixed'</span></span>
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921
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<pre style="margin: 0;"> <span id="LC921" 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;">shlex</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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914
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="python"> <span class="n" style="color: #333;">declarations</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">p</span><span class="p">[</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;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">]])</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="919" 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="927" 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">@@ -919,7 +927,7 @@ class WiggleReader( FileOrSequence ):</td>
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919
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927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="python"> <span class="n" style="color: #333;">span</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;">declarations</span><span class="p">[</span><span class="s" style="color: #d14;">'span'</span><span class="p">])</span></span>
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<td class="diff-line-num old_line" data-linenumber="920" 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">
920
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<td class="diff-line-num new_line" data-linenumber="928" 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">
928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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921
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<td class="diff-line-num new_line" data-linenumber="929" 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">
929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="python"> <span class="n" style="color: #333;">span</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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922
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<td class="diff-line-num new_line old" data-linenumber="930" 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="LC922" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'variableStep'</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">):</span></span> <span class="c" style="color: #998; font-style: italic;"># do variable step stuff</span></span>
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<td class="diff-line-num new old_line" data-linenumber="923" 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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<td class="diff-line-num new new_line" data-linenumber="930" 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">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">'variableStep'</span></span><span class="p"><span class="idiff">):</span></span><span class="idiff right"> </span> <span class="c" style="color: #998; font-style: italic;"># do variable step stuff</span></span>
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923
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931
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stepType</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'variable'</span></span>
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924
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932
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<pre style="margin: 0;"> <span id="LC932" 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;">shlex</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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925
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933
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="python"> <span class="n" style="color: #333;">declarations</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">p</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">p</span><span class="p">[</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;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">'"'</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">]])</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="928" 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="936" 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">@@ -928,124 +936,132 @@ class WiggleReader( FileOrSequence ):</td>
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928
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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="python"> <span class="n" style="color: #333;">span</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;">declarations</span><span class="p">[</span><span class="s" style="color: #d14;">'span'</span><span class="p">])</span></span>
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929
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937
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<pre style="margin: 0;"> <span id="LC937" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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930
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="python"> <span class="n" style="color: #333;">span</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 old old_line" data-linenumber="931" 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">
931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff">'browser'</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startswith</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'#'</span></span><span class="idiff"> </span><span class="p"><span class="idiff">):</span></span><span class="idiff"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right">#</span>Comment or ignored</span></span>
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<td class="diff-line-num new old_line" data-linenumber="932" 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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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">'browser'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startswith</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'#'</span></span><span class="p"><span class="idiff">):</span></span><span class="idiff"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right"># </span>Comment or ignored</span></span>
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932
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940
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<pre style="margin: 0;"> <span id="LC940" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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933
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941
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Ignored line:"</span><span class="p">,</span> <span class="n" style="color: #333;">line</span></span>
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934
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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944
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stepType</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'fixed'</span><span class="p">:</span></span>
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937
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">GenomicInterval</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</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">span</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'.'</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">GenomicInterval</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chrom</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos</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">span</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'.'</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff right">())</span>)</span></span>
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938
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<pre style="margin: 0;"> <span id="LC946" class="line" lang="python"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">step</span></span>
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stepType</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'variable'</span><span class="p">:</span></span>
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940
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948
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="python"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">)</span></span>
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941
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949
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<pre style="margin: 0;"> <span id="LC949" class="line" lang="python"> <span class="n" style="color: #333;">pos</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;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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942
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<pre style="margin: 0;">-<span id="LC942" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">pos</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;">span</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span> <span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">)</span></span>
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943
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<pre style="margin: 0;">-<span id="LC943" class="line" lang="python"> </span>
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944
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BAM_Reader</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">object</span> <span class="p">):</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">pos</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;">span</span><span class="p">,</span> <span class="s" style="color: #d14;">'.'</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="python"></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BAM_Reader</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">pysam</span></span>
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span></span>
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c" style="color: #998; font-style: italic;"># This one is only used by __getitem__</span></span>
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_sq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_sq</span></span>
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<pre style="margin: 0;"> <span id="LC961" 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="LC952" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="python"> <span class="idiff left right"> </span><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">write</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Please Install PySam to use the BAM_Reader Class (http://code.google.com/p/pysam/)"</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC957" 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="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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="LC964" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">write</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff right">"Please Install PySam to use the BAM_Reader Class (http://code.google.com/p/pysam/)"</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC967" 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;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">check_sq</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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970
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pa</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sf</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#yield SAM_Alignment.from_pysam_AlignedRead(<span class="idiff left right"> pa, sf </span>)</span></span>
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962
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">SAM_Alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_pysam_AlignedSegment</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">pa</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sf</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#yield SAM_Alignment.from_pysam_AlignedRead(<span class="idiff left right">pa, sf</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">SAM_Alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_pysam_AlignedSegment</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">pa</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sf</span></span><span class="p">)</span></span>
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC964" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">region</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC966" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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="LC974" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">region</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="LC976" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">check_sq</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</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="LC978" 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="LC969" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pa</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fetch</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reference</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><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">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">region</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC970" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">yield</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">SAM_Alignment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">from_pysam_AlignedRead</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pa</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sf</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC971" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</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 new new_line" data-linenumber="979" 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">
979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pa</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sf</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fetch</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">reference</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><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">end</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">region</span></span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="980" 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">
980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">yield</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">SAM_Alignment</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">from_pysam_AlignedRead</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pa</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">sf</span></span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="972" 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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<td class="diff-line-num new new_line" data-linenumber="981" 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">
981
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC981" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</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 old_line" data-linenumber="972" 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">
972
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<td class="diff-line-num new_line" data-linenumber="982" 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">
982
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<pre style="margin: 0;"> <span id="LC982" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="973" 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">
973
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<td class="diff-line-num new_line old" data-linenumber="983" 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="LC973" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fetch called on bamfile without index"</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="974" 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">
974
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<td class="diff-line-num new_line old" data-linenumber="983" 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="LC974" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Error: "</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">message</span></span>
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<td class="diff-line-num old old_line" data-linenumber="975" 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">
975
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<td class="diff-line-num new_line old" data-linenumber="983" 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="LC975" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Your bam index file is missing or wrongly named, convention is that file 'x.bam' has index file 'x.bam.bai'!"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="976" 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">
976
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<td class="diff-line-num new_line old" data-linenumber="983" 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="LC976" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="977" 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">
977
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<td class="diff-line-num new_line old" data-linenumber="983" 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="LC977" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<td class="diff-line-num new old_line" data-linenumber="978" 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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<td class="diff-line-num new new_line" data-linenumber="983" 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">
983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">message</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fetch called on bamfile without index"</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="984" 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">
984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Error: "</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">message</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="985" 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">
985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Your bam index file is missing or wrongly named, convention is that file 'x.bam' has index file 'x.bam.bai'!"</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">raise</span></span>
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978
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988
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<pre style="margin: 0;"> <span id="LC988" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="python"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">raise</span></span>
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980
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990
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<pre style="margin: 0;"> <span id="LC990" class="line" lang="python"></span>
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981
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<td class="diff-line-num new_line old" data-linenumber="991" 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="LC981" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_line_number_string</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_line_number_string</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left right">self</span></span><span class="p">):</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC992" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">==</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="LC983" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"unopened file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"unopened file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">filename</span></span><span class="p">)</span></span>
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984
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994
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<pre style="margin: 0;"> <span id="LC994" 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="LC985" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"record #</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d in file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">record_no</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">iv</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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988
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<pre style="margin: 0;">-<span id="LC988" 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;">isinstance</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">iv</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">GenomicInterval</span></span><span class="idiff right"> </span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">raise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">TypeError</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"Use a HTSeq.GenomicInterval to access regions within .bam-file!"</span></span><span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"record #</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d in file </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">record_no</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">filename</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">iv</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC998" 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;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">iv</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">GenomicInterval</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="python"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">raise</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">TypeError</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Use a HTSeq.GenomicInterval to access regions within .bam-file!"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</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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<pre style="margin: 0;">-<span id="LC991" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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="LC992" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># NOTE: pysam 0.9 has renames _hasIndex into has_index</span></span>
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</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;">sf</span><span class="p">,</span> <span class="s" style="color: #d14;">'_hasIndex'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_hasIndex</span><span class="p">()))</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_index</span><span class="p">()):</span></span>
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"The .bam-file has no index, random-access is disabled!"</span></span>
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995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pa</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">SAM_Alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_pysam_AlignedRead</span><span class="p">(</span> <span class="n" style="color: #333;">pa</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;">sf</span> <span class="p">)</span></span>
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997
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="python"> </span>
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998
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_header_dict</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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999
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span></span>
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1000
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">header</span></span>
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1001
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="python"> </span>
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1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="python"> </span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BAM_Writer</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">object</span> <span class="p">):</span></span>
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1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">template</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;">referencenames</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;">referencelengths</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;">text</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;">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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1005
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"Please Install PySam to use the BAM_Writer Class (http://code.google.com/p/pysam/)"</span> <span class="p">)</span></span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="python"> </span>
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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span></span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template</span></span>
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">referencenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">referencenames</span></span>
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">referencelengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">referencelengths</span></span>
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">text</span></span>
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span></span>
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<pre style="margin: 0;">-<span id="LC1017" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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;">"wb"</span><span class="p">,</span> <span class="n" style="color: #333;">template</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;">template</span><span class="p">,</span> <span class="n" style="color: #333;">referencenames</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;">referencenames</span><span class="p">,</span> <span class="n" style="color: #333;">referencelengths</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;">referencelengths</span><span class="p">,</span> <span class="n" style="color: #333;">text</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;">text</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;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">header</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1018" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_BAM_Reader</span><span class="p">(</span> <span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="n" style="color: #333;">br</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1021" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">BAM_Writer</span><span class="p">(</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_header_dict</span><span class="p">()</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1022" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC1023" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">alnmt</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1024" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#self.sf.write( alnmt.to_pysam_AlignedRead( self.sf ) )</span></span>
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<pre style="margin: 0;">-<span id="LC1025" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="n" style="color: #333;">alnmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_pysam_AlignedSegment</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;">sf</span> <span class="p">)</span> <span class="p">)</span></span>
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1026
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<pre style="margin: 0;">-<span id="LC1026" class="line" lang="python"> </span>
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<pre style="margin: 0;">-<span id="LC1027" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</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="LC1028" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BED_Reader</span><span class="p">(</span> <span class="n" style="color: #333;">FileOrSequence</span> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC1032" class="line" lang="python"></span>
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1033
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1033" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span> <span class="p">):</span></span>
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1034
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1034" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span> <span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1035" 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">
1035
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1035" class="line" lang="python"> </span>
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1036
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1036" 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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<td class="diff-line-num old old_line" data-linenumber="1037" 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">
1037
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1037" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1038" 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">
1038
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1038" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="s" style="color: #d14;">"track"</span> <span class="p">):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1039" 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">
1039
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1039" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1040" 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">
1040
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1040" 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;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1041" 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">
1041
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1041" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1042" 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">
1042
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1042" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"BED file line contains less than 3 fields"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1043" 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">
1043
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1043" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1044" 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">
1044
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1044" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"BED file line contains more than 9 fields"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1045" 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">
1045
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1045" class="line" lang="python"> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"."</span> <span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1046" 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">
1046
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1046" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicFeature</span><span class="p">(</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"unnamed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"BED line"</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span> <span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1047" 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">
1047
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1047" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1048" 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">
1048
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<td class="diff-line-num new_line old" data-linenumber="1001" 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="LC1048" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">thick</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="p">),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="p">),</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">7</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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1049
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<pre style="margin: 0;">-<span id="LC1049" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemRgb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span> <span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">,</span> <span class="n" style="color: #333;">check_sq</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;">check_sq</span><span class="p">)</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># NOTE: pysam 0.9 has renames _hasIndex into has_index</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</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;">sf</span><span class="p">,</span> <span class="s" style="color: #d14;">'_hasIndex'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_hasIndex</span><span class="p">()))</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_index</span><span class="p">()):</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"The .bam-file has no index, random-access is disabled!"</span><span class="p">)</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pa</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end</span><span class="p">):</span></span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">SAM_Alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_pysam_AlignedRead</span><span class="p">(</span><span class="n" style="color: #333;">pa</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;">sf</span><span class="p">)</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="python"></span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_header_dict</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">,</span> <span class="n" style="color: #333;">check_sq</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;">check_sq</span><span class="p">)</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">header</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="python"></span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="python"></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BAM_Writer</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">template</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;">referencenames</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;">referencelengths</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;">text</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;">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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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Please Install PySam to use the BAM_Writer Class (http://code.google.com/p/pysam/)"</span><span class="p">)</span></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1021" 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">
1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1022" 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">
1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1023" 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">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">referencenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">referencenames</span></span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">referencelengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">referencelengths</span></span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">text</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1026" 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">
1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span></span>
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1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1029" 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">
1029
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<pre style="margin: 0;">+<span id="LC1029" 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;">"wb"</span><span class="p">,</span></span>
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1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="python"> <span class="n" style="color: #333;">template</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;">template</span><span class="p">,</span></span>
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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="python"> <span class="n" style="color: #333;">referencenames</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;">referencenames</span><span class="p">,</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="python"> <span class="n" style="color: #333;">referencelengths</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;">referencelengths</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1033" 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">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="python"> <span class="n" style="color: #333;">text</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;">text</span><span class="p">,</span></span>
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1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="python"> <span class="n" style="color: #333;">header</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;">header</span><span class="p">)</span></span>
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1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="python"></span>
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1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1037" 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">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_BAM_Reader</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="n" style="color: #333;">br</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1038" 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">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">BAM_Writer</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">br</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_header_dict</span><span class="p">())</span></span>
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1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="python"></span>
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1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">alnmt</span><span class="p">):</span></span>
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1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;">#self.sf.write(alnmt.to_pysam_AlignedRead(self.sf))</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">alnmt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">to_pysam_AlignedSegment</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;">sf</span><span class="p">))</span></span>
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1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="python"></span>
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1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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1051
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="python"></span>
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1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="1048" 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">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BED_Reader</span><span class="p">(</span><span class="n" style="color: #333;">FileOrSequence</span><span class="p">):</span></span>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="python"></span>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span><span class="p">):</span></span>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="python"> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename_or_sequence</span><span class="p">)</span></span>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="python"></span>
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1053
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<pre style="margin: 0;">+<span id="LC1053" 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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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"track"</span><span class="p">):</span></span>
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1056
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<pre style="margin: 0;">+<span id="LC1056" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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1057
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<pre style="margin: 0;">+<span id="LC1057" 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;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"BED file line contains less than 3 fields"</span><span class="p">)</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1061" 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">
1061
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<pre style="margin: 0;">+<span id="LC1061" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"BED file line contains more than 9 fields"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1062" 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">
1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="python"> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]),</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"."</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1063" 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">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicFeature</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"unnamed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"BED line"</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1064" 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">
1064
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<pre style="margin: 0;">+<span id="LC1064" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1065" 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">
1065
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<pre style="margin: 0;">+<span id="LC1065" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">thick</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GenomicInterval</span><span class="p">(</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]),</span> <span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">7</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">itemRgb</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#e860acebd843648e033662eac1a1d0620e7dc6d7"><strong>python2/HTSeq/_version.py</strong></a>
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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;">"0.9.1"</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;">"0.10.0"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#48d1d1c7549dfe506a0f860bd23b62c026693628"><strong>python2/HTSeq/scripts/count.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">@@ -87,6 +87,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <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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88
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100000</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="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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89
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d GFF lines processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">i</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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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91
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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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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92
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when processing GFF file (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" 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="96" 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">@@ -95,6 +96,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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95
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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96
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97
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<pre style="margin: 0;"> <span id="LC97" 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;">quiet</span><span class="p">:</span></span>
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97
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d GFF lines processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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98
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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99
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">)</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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100
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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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="158" 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">@@ -156,6 +158,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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156
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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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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157
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d SAM alignment record</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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158
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"s"</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" pairs"</span><span class="p">))</span></span>
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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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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159
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>
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160
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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;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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161
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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;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" 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="301" 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">@@ -298,6 +301,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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299
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d SAM </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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300
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"alignments "</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"alignment pairs"</span><span class="p">))</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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301
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"></span>
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302
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samoutfile</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="p">:</span></span>
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303
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">samoutfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<li id="fc97c7539c2f5e31f663b33a263013f82d8eac33">
<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#fc97c7539c2f5e31f663b33a263013f82d8eac33"><strong>python2/src/HTSeq/_HTSeq.pyx</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">@@ -576,7 +576,9 @@ cdef class GenomicArray(object):</td>
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576
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="plaintext"> self.storage, self.memmap_dir)</span>
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577
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="plaintext"> else:</span>
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578
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="plaintext"> self.chrom_vectors[chrom] = {</span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="plaintext"> strand_nostrand: ChromVector.create(iv, self.typecode, self.storage)}</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext"> strand_nostrand: ChromVector.create(iv, self.typecode,</span>
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> self.storage,</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext"> self.memmap_dir)}</span>
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="plaintext"></span>
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581
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="plaintext"> def __reduce__(self):</span>
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="plaintext"> return (_GenomicArray_unpickle, (self.stranded, self.typecode, self.chrom_vectors))</span>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#5f8bf900fa412d21d637ab1c77a631a00551279d"><strong>python3/HTSeq/__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">@@ -993,11 +993,12 @@ class WiggleReader(FileOrSequence):</td>
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<pre style="margin: 0;"> <span id="LC993" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC994" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BAM_Reader</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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995
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<pre style="margin: 0;"> <span id="LC995" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>
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997
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<pre style="margin: 0;"> <span id="LC997" class="line" lang="python"> <span class="k" style="font-weight: 600;">global</span> <span class="n" style="color: #333;">pysam</span></span>
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<pre style="margin: 0;"> <span id="LC998" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span></span>
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<pre style="margin: 0;"> <span id="LC999" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c" style="color: #998; font-style: italic;"># This one is only used by __getitem__</span></span>
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_sq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_sq</span></span>
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<pre style="margin: 0;"> <span id="LC1002" 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="LC1003" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;"> <span id="LC1004" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</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">@@ -1006,7 +1007,7 @@ class BAM_Reader(object):</td>
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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1009" 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="LC1009" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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="LC1010" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">check_sq</span></span><span class="p">)</span></span>
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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1011
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pa</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sf</span><span class="p">:</span></span>
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># yield SAM_Alignment.from_pysam_AlignedRead( pa, sf )</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">@@ -1014,7 +1015,7 @@ class BAM_Reader(object):</td>
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fetch</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">reference</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;">start</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;">end</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;">region</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="LC1017" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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="LC1018" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">check_sq</span></span><span class="p">)</span></span>
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1018
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1019
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<pre style="margin: 0;"> <span id="LC1019" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">record_no</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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1019
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1020
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<pre style="margin: 0;"> <span id="LC1020" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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1020
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pa</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">reference</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;">region</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1041" 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="1042" 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">@@ -1041,7 +1042,7 @@ class BAM_Reader(object):</td>
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1041
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">TypeError</span><span class="p">(</span></span>
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1042
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1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="python"> <span class="s" style="color: #d14;">"Use a HTSeq.GenomicInterval to access regions within .bam-file!"</span><span class="p">)</span></span>
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1043
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1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</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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<pre style="margin: 0;">-<span id="LC1044" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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="LC1045" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">check_sq</span></span><span class="p">)</span></span>
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1046
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="python"> <span class="c" style="color: #998; font-style: italic;"># NOTE: pysam 0.9 has renames _hasIndex into has_index</span></span>
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1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</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;">sf</span><span class="p">,</span> <span class="s" style="color: #d14;">'_hasIndex'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_hasIndex</span><span class="p">()))</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_index</span><span class="p">()):</span></span>
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1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1051" 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">@@ -1050,7 +1051,7 @@ class BAM_Reader(object):</td>
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1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">SAM_Alignment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">from_pysam_AlignedRead</span><span class="p">(</span><span class="n" style="color: #333;">pa</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;">sf</span><span class="p">)</span></span>
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_header_dict</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="LC1053" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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="LC1054" class="line" lang="python"> <span class="n" style="color: #333;">sf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</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;">filename</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">check_sq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">check_sq</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sf</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">header</span></span>
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#6ef6a1ad5db69d445d8356610d7f345cb83afe6a"><strong>python3/HTSeq/_version.py</strong></a>
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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;">"0.9.1"</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;">"0.10.0"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#e5673f04e9098a0bf1f4da138b373b347616dfe0"><strong>python3/HTSeq/scripts/count.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="87" 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="87" 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">@@ -87,6 +87,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <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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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100000</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="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">quiet</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="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d GFF lines processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">i</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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when processing GFF file (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</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">@@ -95,6 +96,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC97" 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;">quiet</span><span class="p">:</span></span>
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97
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d GFF lines processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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98
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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99
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">)</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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100
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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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="156" 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="158" 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">@@ -156,6 +158,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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156
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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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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157
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<td class="diff-line-num new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d SAM alignment record</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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158
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<td class="diff-line-num new_line" data-linenumber="160" 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">
160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"s"</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" pairs"</span><span class="p">))</span></span>
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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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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159
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>
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160
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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;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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161
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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;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="298" 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="301" 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">@@ -298,6 +301,7 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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298
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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299
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d SAM </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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300
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<td class="diff-line-num new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"alignments "</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"alignment pairs"</span><span class="p">))</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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301
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"></span>
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302
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samoutfile</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="p">:</span></span>
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303
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">samoutfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#a8dcb9b2f363c919df57f4b82171ac5afa3861eb"><strong>python3/src/HTSeq/_HTSeq.pyx</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">@@ -579,7 +579,9 @@ cdef class GenomicArray(object):</td>
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579
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="plaintext"> self.storage, self.memmap_dir)</span>
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="plaintext"> else:</span>
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="plaintext"> self.chrom_vectors[chrom] = {</span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="plaintext"> strand_nostrand: ChromVector.create(iv, self.typecode, self.storage)}</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext"> strand_nostrand: ChromVector.create(iv, self.typecode,</span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext"> self.storage,</span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext"> self.memmap_dir)}</span>
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585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="plaintext"> def __reduce__(self):</span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="plaintext"> return (_GenomicArray_unpickle, (self.stranded, self.typecode, self.chrom_vectors))</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1513" 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">@@ -1513,12 +1515,19 @@ cdef class SAM_Alignment(AlignmentWithSequenceReversal):</td>
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<pre style="margin: 0;"> <span id="LC1515" class="line" lang="plaintext"> else:</span>
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<pre style="margin: 0;"> <span id="LC1516" class="line" lang="plaintext"> cigar = "*"</span>
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC1516" class="line" lang="plaintext"> return '\t'.join((self.read.name, str(self.flag), query_start.chrom,</span>
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<pre style="margin: 0;">-<span id="LC1517" class="line" lang="plaintext"> str(query_start.start +</span>
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<pre style="margin: 0;">-<span id="LC1518" class="line" lang="plaintext"> 1), str(self.aQual), cigar, mate_start.chrom,</span>
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<pre style="margin: 0;">-<span id="LC1519" class="line" lang="plaintext"> str(mate_start.pos + 1), str(self.inferred_insert_size),</span>
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<pre style="margin: 0;">-<span id="LC1520" class="line" lang="plaintext"> self.read_as_aligned.seq, self.read_as_aligned.qualstr,</span>
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<pre style="margin: 0;">-<span id="LC1521" class="line" lang="plaintext"> '\t'.join(self.raw_optional_fields())))</span>
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="plaintext"> return '\t'.join(</span>
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="plaintext"> (self.read.name,</span>
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="plaintext"> str(self.flag),</span>
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="plaintext"> query_start.chrom,</span>
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1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="plaintext"> str(query_start.start + 1),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1523" 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">
1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="plaintext"> str(self.aQual),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1522" 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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<td class="diff-line-num new new_line" data-linenumber="1524" 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">
1524
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<pre style="margin: 0;">+<span id="LC1524" class="line" lang="plaintext"> cigar,</span>
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<td class="diff-line-num new old_line" data-linenumber="1522" 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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<td class="diff-line-num new new_line" data-linenumber="1525" 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">
1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="plaintext"> mate_start.chrom,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1522" 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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<td class="diff-line-num new new_line" data-linenumber="1526" 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">
1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="plaintext"> str(mate_start.pos + 1),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1522" 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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<td class="diff-line-num new new_line" data-linenumber="1527" 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">
1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="plaintext"> str(self.inferred_insert_size),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1522" 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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<td class="diff-line-num new new_line" data-linenumber="1528" 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">
1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="plaintext"> self.read_as_aligned.seq.decode(),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1522" 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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<td class="diff-line-num new new_line" data-linenumber="1529" 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">
1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="plaintext"> self.read_as_aligned.qualstr.decode(),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1530" 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">
1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="plaintext"> '\t'.join(self.raw_optional_fields())))</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1522" 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">
1522
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1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1523" 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">
1523
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1532
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="plaintext"> def optional_field(SAM_Alignment self, str tag):</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1524" 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">
1524
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1533
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="plaintext"> res = [p for p in self.optional_fields if p[0] == tag]</span>
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<a href="https://salsa.debian.org/med-team/htseq/compare/ca6807052dce671b9c96149b9c0468f9826ef5b4...ebb0d026ee514e57bb49f887ccf09bcd5129203a#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">[egg_info]</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">tag_build = </span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">tag_date = 0</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">tag_svn_revision = 0</span>
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5
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span></pre>
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