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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pyvcf">Debian Med / python-pyvcf</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/-/commit/c9306f6db6b0fe96a6136d98410995105ceef162">c9306f6d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-15T12:44:47+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix FTBFS with new setuptools
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/-/commit/f8210ba398017aabbdd6316b68c08c417592b60b">f8210ba3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-15T12:45:02+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change python2 syntax to python3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/-/commit/d39b52f81075427dd093edaaa056ef0756c7bf35">d39b52f8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-15T12:47:52+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: change homepage to github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/-/commit/e5bb48d126a2b6b21968c85be76ee2c29bc5d69a">e5bb48d1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-15T12:49:11+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump debhelper compatibility level to 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/-/commit/5ed6c928ca131150dab7dfb9d548bd694cf4f6a5">5ed6c928</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-15T12:49:31+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump Standards-Version to 4.6.0 (no changes needed)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/-/commit/7320172b3cf697c9bbbe92031770bf58576dee18">7320172b</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-15T12:50:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add "Rules-Requires-Root: no"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/-/commit/19638e8dcd106affcb14664b0f420808d1f58f1d">19638e8d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-10-15T12:52:39+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#266c1a3b897df10ca4524ab8d9bd7b7f032a3913">
<span class="new-file">
+
debian/patches/fix-setuptools.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pyvcf/-/compare/bf9274b528d8ac3aacd8336e617c02ab36836bd3...19638e8dcd106affcb14664b0f420808d1f58f1d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pyvcf (0.6.8+git20170215.476169c-8) unstable; urgency=medium</span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * d/patches:</span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> - fix-setuptools.patch: Fix FTBFS with new setuptools</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="1" 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="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> - 2to3.patch: Change python2 syntax to python3</span>
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<td class="old_line diff-line-num new" data-linenumber="1" 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="new_line diff-line-num new" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * d/control:</span>
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<td class="new_line diff-line-num new" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> - Change homepage to github</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1" 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="new_line diff-line-num new" data-linenumber="9" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> - Bump debhelper compatibility level to 13</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1" 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="LC10" class="line" lang="plaintext"> - Bump Standards-Version to 4.6.0 (no changes needed)</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="1" 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="new_line diff-line-num new" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> - Add "Rules-Requires-Root: no"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Fri, 15 Oct 2021 12:51:04 +0530</span>
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<td class="new_line diff-line-num new" data-linenumber="14" 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="LC14" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="15" 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="LC15" class="line" lang="plaintext">python-pyvcf (0.6.8+git20170215.476169c-7) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Test-Depends: python3-pytest</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/python-pyvcf/-/compare/bf9274b528d8ac3aacd8336e617c02ab36836bd3...19638e8dcd106affcb14664b0f420808d1f58f1d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,17 +4,18 @@ Uploaders: Andreas Tille <tille@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: python</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-pysam <!nocheck>,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5</span>.0</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6</span>.0</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-pyvcf</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-pyvcf.git</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Homepage: https://pypi.python.org/pypi/PyVCF</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Homepage: https://github.com/jamescasbon/PyVCF</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: python3-vcf</span>
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20
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: any</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/python-pyvcf/-/compare/bf9274b528d8ac3aacd8336e617c02ab36836bd3...19638e8dcd106affcb14664b0f420808d1f58f1d#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Convert python2 syntax to python3</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2021-10-15</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/conf.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -40,8 +40,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> master_doc = 'index'</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> # General information about the project.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-project = u'PyVCF'</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-copyright = u'2012, James Casbon, @jdoughertyii'</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project = 'PyVCF'</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+copyright = '2012, James Casbon, @jdoughertyii'</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> # The version info for the project you're documenting, acts as replacement for</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> # |version| and |release|, also used in various other places throughout the</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -179,8 +179,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> # Grouping the document tree into LaTeX files. List of tuples</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> # (source start file, target name, title, author, documentclass [howto/manual]).</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> latex_documents = [</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'PyVCF.tex', u'PyVCF Documentation',</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- u'James Casbon, @jdoughertyii', 'manual'),</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'PyVCF.tex', 'PyVCF Documentation',</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'James Casbon, @jdoughertyii', 'manual'),</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> # The name of an image file (relative to this directory) to place at the top of</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -212,6 +212,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> # One entry per manual page. List of tuples</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> # (source start file, name, description, authors, manual section).</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> man_pages = [</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ('index', 'pyvcf', u'PyVCF Documentation',</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [u'James Casbon, @jdoughertyii'], 1)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ('index', 'pyvcf', 'PyVCF Documentation',</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ['James Casbon, @jdoughertyii'], 1)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> ]</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/vcf_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/vcf_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -108,7 +108,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> while len(args.rest):</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> filter_name = args.rest.pop(0)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> if filter_name not in filters:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.exit("%s is not a known filter (%s)" % (filter_name, str(filters.keys())))</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sys.exit("%s is not a known filter (%s)" % (filter_name, str(list(filters.keys()))))</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> # create a parser only for arguments of current filter</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> filt_parser = create_filt_parser(filter_name)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/vcf_sample_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/vcf_sample_filter.py</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="p">@@ -34,6 +34,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> sf = SampleFilter(infile=args.file, outfile=args.o,</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> filters=args.f, invert=args.invert)</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> if args.f is None:</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Samples:"</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Samples:")</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> for idx, val in enumerate(sf.samples):</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "{0}: {1}".format(idx, val)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("{0}: {1}".format(idx, val))</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/vcf/model.py</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/vcf/model.py</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -362,7 +362,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> If there are i alleles with frequency p_i, H=1-sum_i(p_i^2)</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> allele_freqs = [1-sum(self.aaf)] + self.aaf</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return 1 - sum(map(lambda x: x**2, allele_freqs))</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return 1 - sum([x**2 for x in allele_freqs])</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> def get_hom_refs(self):</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> """ The list of hom ref genotypes"""</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -558,9 +558,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> return True</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class _AltRecord(object):</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class _AltRecord(object, metaclass=ABCMeta):</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> '''An alternative allele record: either replacement string, SV placeholder, or breakend'''</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __metaclass__ = ABCMeta</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> def __init__(self, type, **kwargs):</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> super(_AltRecord, self).__init__(**kwargs)</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -596,7 +595,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> return len(self.sequence)</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> def __eq__(self, other):</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if isinstance(other, basestring):</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if isinstance(other, str):</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> return self.sequence == other</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> elif not isinstance(other, self.__class__):</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> return False</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/vcf/parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/vcf/parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -22,8 +22,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> except ImportError:</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> cparse = None</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from model import _Call, _Record, make_calldata_tuple</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from model import _Substitution, _Breakend, _SingleBreakend, _SV</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .model import _Call, _Record, make_calldata_tuple</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .model import _Substitution, _Breakend, _SingleBreakend, _SV</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> # Metadata parsers/constants</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -468,7 +468,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> nfields = len(samp_fmt._fields)</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for name, sample in itertools.izip(self.samples, samples):</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for name, sample in zip(self.samples, samples):</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> </span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> # parse the data for this sample</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> sampdat = [None] * nfields</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -548,7 +548,7 @@</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> return _Substitution(str)</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- def next(self):</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ def __next__(self):</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> '''Return the next record in the file.'''</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> line = next(self.reader)</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> row = self._row_pattern.split(line.rstrip())</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -641,7 +641,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> """VCF Writer. On Windows Python 2, open stream with 'wb'."""</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> # Reverse keys and values in header field count dictionary</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- counts = dict((v,k) for k,v in field_counts.iteritems())</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ counts = dict((v,k) for k,v in field_counts.items())</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> def __init__(self, stream, template, lineterminator="\n"):</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> self.writer = csv.writer(stream, delimiter="\t",</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="p">@@ -654,30 +654,30 @@</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> # get a maximum key).</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> self.info_order = collections.defaultdict(</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> lambda: len(template.infos),</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dict(zip(template.infos.iterkeys(), itertools.count())))</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ dict(list(zip(iter(template.infos.keys()), itertools.count()))))</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> </span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> two = '##{key}=<ID={0},Description="{1}">\n'</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> four = '##{key}=<ID={0},Number={num},Type={2},Description="{3}">\n'</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> _num = self._fix_field_count</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (key, vals) in template.metadata.iteritems():</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (key, vals) in template.metadata.items():</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> if key in SINGULAR_METADATA:</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> vals = [vals]</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> for val in vals:</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> if isinstance(val, dict):</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> values = ','.join('{0}={1}'.format(key, value)</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key, value in val.items())</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key, value in list(val.items()))</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> stream.write('##{0}=<{1}>\n'.format(key, values))</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> else:</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> stream.write('##{0}={1}\n'.format(key, val))</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in template.infos.itervalues():</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in template.infos.values():</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> stream.write(four.format(key="INFO", *line, num=_num(line.num)))</span>
</pre>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in template.formats.itervalues():</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in template.formats.values():</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> stream.write(four.format(key="FORMAT", *line, num=_num(line.num)))</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in template.filters.itervalues():</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in template.filters.values():</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> stream.write(two.format(key="FILTER", *line))</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in template.alts.itervalues():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in template.alts.values():</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> stream.write(two.format(key="ALT", *line))</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for line in template.contigs.itervalues():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for line in template.contigs.values():</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> if line.length:</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> stream.write('##contig=<ID={0},length={1}>\n'.format(*line))</span>
</pre>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> else:</span>
</pre>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/vcf/sample_filter.py</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/vcf/sample_filter.py</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> import warnings</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> </span>
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<td class="new_line diff-line-num new" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> </span>
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<td class="new_line diff-line-num new" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from parser import Reader, Writer</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .parser import Reader, Writer</span></span>
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<td class="new_line diff-line-num new" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> class SampleFilter(object):</span>
</pre>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="p">@@ -81,13 +81,13 @@</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> # is int, check if it's an idx</span>
</pre>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> if item < len(self.samples):</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> return item</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- filters = set(filter(lambda x: x is not None, map(filt2idx, filt_s)))</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filters = set([x for x in map(filt2idx, filt_s) if x is not None])</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> if len(filters) < len(filt_s):</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> # TODO print the filters that were ignored</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> warnings.warn("Invalid filters, ignoring", RuntimeWarning)</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> </span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> if self.invert:</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- filters = set(xrange(len(self.samples))).difference(filters)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filters = set(range(len(self.samples))).difference(filters)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> </span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> # `sample_filter` setter updates `samples`</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> self.parser.sample_filter = filters</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/vcf/test/prof.py</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/vcf/test/prof.py</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> elif sys.argv[1] == 'time':</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> n = 1</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> t = timeit.timeit('parse_1kg()', "from __main__ import parse_1kg", number=n)</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print t/n</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(t/n)</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> </span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> elif sys.argv[1] == 'stat':</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> import statprof</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="p">@@ -30,4 +30,4 @@</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> statprof.stop()</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> statprof.display()</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> else:</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'prof.py profile/time'</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('prof.py profile/time')</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/vcf/test/test_vcf.py</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/vcf/test/test_vcf.py</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> import unittest</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> try:</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> unittest.skip</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -6,9 +6,9 @@</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> import unittest2 as unittest</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> import doctest</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> import os</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import commands</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from StringIO import StringIO</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import subprocess</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from io import StringIO</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> import subprocess</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="p">@@ -137,7 +137,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> """Test VCF inputs with ##contig inputs containing only IDs. produced by bcftools 1.2+</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> reader = vcf.Reader(fh("contig_idonly.vcf"))</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for cid, contig in reader.contigs.items():</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for cid, contig in list(reader.contigs.items()):</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> if cid == "1":</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> assert contig.length is None</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> elif cid == "2":</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="p">@@ -390,24 +390,24 @@</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> reader2 = vcf.Reader(out)</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> for l, r in zip(records, reader2):</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(l.INFO, r.INFO)</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(l.INFO, r.INFO)</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> class TestBadInfoFields(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> def test_parse(self):</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> reader = vcf.Reader(fh('bad-info-character.vcf'))</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> record = next(reader)</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['DOT_1'], None)</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['DOT_3'], [None, None, None])</span></span>
</pre>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['DOT_N'], [None])</span></span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['EMPTY_1'], None)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['DOT_1'], None)</span></span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['DOT_3'], [None, None, None])</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['DOT_N'], [None])</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['EMPTY_1'], None)</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> # Perhaps EMPTY_3 should yield [None, None, None] but this is really a</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="264" 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">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> # cornercase of unspecified behaviour.</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['EMPTY_3'], [None])</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['EMPTY_N'], [None])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['NOTEMPTY_1'], 1)</span></span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['NOTEMPTY_3'], [1, 2, 3])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(record.INFO['NOTEMPTY_N'], [1])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="270" 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">
270
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['EMPTY_3'], [None])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['EMPTY_N'], [None])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="272" 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">
272
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['NOTEMPTY_1'], 1)</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="273" 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">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['NOTEMPTY_3'], [1, 2, 3])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(record.INFO['NOTEMPTY_N'], [1])</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> pass</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="277" 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">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> </span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="p">@@ -440,7 +440,7 @@</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> self.assertEqual(f['Options'], '"< 4 and > 3"')</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="280" 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">
280
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> </span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="281" 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">
281
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> for l, r in zip(records, reader2):</span>
</pre>
</td>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(l.INFO, r.INFO)</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(l.INFO, r.INFO)</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> </span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> </span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> class TestGatkOutputWriter(unittest.TestCase):</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="p">@@ -463,13 +463,13 @@</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> print (out_str)</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> reader2 = vcf.Reader(out)</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> </span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(reader.samples, reader2.samples)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(reader.formats, reader2.formats)</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(reader.infos, reader2.infos)</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(reader.contigs, reader2.contigs)</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(reader.samples, reader2.samples)</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(reader.formats, reader2.formats)</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(reader.infos, reader2.infos)</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(reader.contigs, reader2.contigs)</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> </span>
</pre>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> for l, r in zip(records, reader2):</span>
</pre>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(l.samples, r.samples)</span></span>
</pre>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(l.samples, r.samples)</span></span>
</pre>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> </span>
</pre>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> # test for call data equality, since equality on the sample calls</span>
</pre>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> # may not always mean their data are all equal</span>
</pre>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="p">@@ -493,12 +493,12 @@</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> print (out.getvalue())</span>
</pre>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> reader2 = vcf.Reader(out)</span>
</pre>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> </span>
</pre>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(reader.samples, reader2.samples)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(reader.formats, reader2.formats)</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(reader.infos, reader2.infos)</span></span>
</pre>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(reader.samples, reader2.samples)</span></span>
</pre>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(reader.formats, reader2.formats)</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(reader.infos, reader2.infos)</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> </span>
</pre>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> for l, r in zip(records, reader2):</span>
</pre>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(l.samples, r.samples)</span></span>
</pre>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(l.samples, r.samples)</span></span>
</pre>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> </span>
</pre>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> # test for call data equality, since equality on the sample calls</span>
</pre>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> # may not always mean their data are all equal</span>
</pre>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="p">@@ -522,7 +522,7 @@</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="324" 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">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> out_str = out.getvalue()</span>
</pre>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> for line in out_str.split("\n"):</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="326" 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">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> if line.startswith("##PEDIGREE"):</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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">
</td>
<td class="new_line diff-line-num new" data-linenumber="327" 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">
327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEquals(line, '##PEDIGREE=<Derived="Tumor",Original="Germline">')</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="328" 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">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(line, '##PEDIGREE=<Derived="Tumor",Original="Germline">')</span></span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="329" 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">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> if line.startswith("##SAMPLE"):</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="330" 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">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> assert line.startswith('##SAMPLE=<'), "Found dictionary in meta line: {0}".format(line)</span>
</pre>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> </span>
</pre>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="p">@@ -955,7 +955,7 @@</span></span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> def test_pickle(self):</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> reader = vcf.Reader(fh('example-4.0.vcf'))</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> for var in reader:</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- self.assertEqual(cPickle.loads(cPickle.dumps(var)), var)</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ self.assertEqual(pickle.loads(pickle.dumps(var)), var)</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> </span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> def assert_has_expected_coordinates(</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="p">@@ -1498,7 +1498,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> @unittest.skip("test currently broken")</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> def testApplyFilter(self):</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> # FIXME: broken with distribute</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq')</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s, out = subprocess.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 test/example-4.0.vcf sq')</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> #print(out)</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> self.assertEqual(s, 0)</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> buf = StringIO()</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="p">@@ -1528,7 +1528,7 @@</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> @unittest.skip("test currently broken")</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> def testApplyMultipleFilters(self):</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> # FIXME: broken with distribute</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- s, out = commands.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 '</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s, out = subprocess.getstatusoutput('python scripts/vcf_filter.py --site-quality 30 '</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> '--genotype-quality 50 test/example-4.0.vcf sq mgq')</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> self.assertEqual(s, 0)</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> #print(out)</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="p">@@ -1599,7 +1599,7 @@</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> assert recs[1] is not None</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"> </span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> # test files with many chromosomes, set 'vcf_record_sort_key' to define chromosome order</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chr_order = map(str, range(1, 30)) + ['X', 'Y', 'M']</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chr_order = list(map(str, list(range(1, 30)))) + ['X', 'Y', 'M']</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> get_key = lambda r: (chr_order.index(r.CHROM.replace('chr','')), r.POS)</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> reader1 = vcf.Reader(fh('issue-140-file1.vcf'))</span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> reader2 = vcf.Reader(fh('issue-140-file2.vcf'))</span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/vcf/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/vcf/utils.py</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="p">@@ -37,19 +37,19 @@</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> next_idx_to_k = dict(</span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> (i, get_key(r)) for i, r in enumerate(nexts) if r is not None)</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> keys_with_prev_contig = [</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- k for k in next_idx_to_k.values() if k[0] == min_k[0]]</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ k for k in list(next_idx_to_k.values()) if k[0] == min_k[0]]</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> if any(keys_with_prev_contig):</span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> min_k = min(keys_with_prev_contig) # finish previous contig</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> min_k = min(next_idx_to_k.values()) # move on to next contig</span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> </span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- min_k_idxs = set([i for i, k in next_idx_to_k.items() if k == min_k])</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ min_k_idxs = set([i for i, k in list(next_idx_to_k.items()) if k == min_k])</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> yield [nexts[i] if i in min_k_idxs else None for i in range(len(nexts))]</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> </span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> for i in min_k_idxs:</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> try:</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- nexts[i] = readers[i].next()</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ nexts[i] = next(readers[i])</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> except StopIteration:</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> nexts[i] = None</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> </span></pre>
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<li id="266c1a3b897df10ca4524ab8d9bd7b7f032a3913">
<a href="https://salsa.debian.org/med-team/python-pyvcf/-/compare/bf9274b528d8ac3aacd8336e617c02ab36836bd3...19638e8dcd106affcb14664b0f420808d1f58f1d#266c1a3b897df10ca4524ab8d9bd7b7f032a3913"><strong>debian/patches/fix-setuptools.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Remove use_2to3 option and languages python 2 and 2.7 from setuptools</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2021-10-15</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -60,8 +60,6 @@</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 'Operating System :: OS Independent',</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 'Programming Language :: Cython',</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 'Programming Language :: Python',</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'Programming Language :: Python :: 2',</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'Programming Language :: Python :: 2.7',</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> 'Programming Language :: Python :: 3',</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 'Programming Language :: Python :: 3.4',</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 'Programming Language :: Python :: 3.5',</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -71,7 +69,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> 'Topic :: Scientific/Engineering :: Bio-Informatics',</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> ],</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> keywords='bioinformatics',</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- use_2to3=True,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> include_package_data=True,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> package_data = {</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> '': ['*.vcf', '*.gz', '*.tbi'],</span></pre>
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<a href="https://salsa.debian.org/med-team/python-pyvcf/-/compare/bf9274b528d8ac3aacd8336e617c02ab36836bd3...19638e8dcd106affcb14664b0f420808d1f58f1d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix-setuptools.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2to3.patch</span></pre>
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