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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/dindel">Debian Med / dindel</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/6dff3369021d15961835d581d173fd6361106ccd">6dff3369</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:27:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/5d6d3666372cb5db2a2a2835150be34caa9c45f2">5d6d3666</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:27:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/601705eef57298a3ac0027dc28b4578f8cd26853">601705ee</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:27:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Remove trailing whitespace in debian/rules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/b72e3cc262f866345876c183d33ea819796a3e98">b72e3cc2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:27:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Add salsa-ci file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/8d49ae70674a56d367800209c12b156deefa5232">8d49ae70</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:27:21+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Rules-Requires-Root: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/5ffa98d237e1fce4f5d6b71800285ed433350d50">5ffa98d2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:27:24+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
Changes-By: lintian-brush
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/874d42cb356c088037a6515f2d0758d9e1ec72be">874d42cb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:27:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: watch file standard 4
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/dd9e9ef60d0df488e6ca84087e6c700f87f13417">dd9e9ef6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T19:57:00+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove boilerplateRemove boilerplate
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/eed7aab2bfb587b902721f013aee86e29082dc72">eed7aab2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T20:03:33+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Call 2to3 on Python scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/dindel/-/commit/d0aa2263b255d495f3598b1e0366cccbeb7b7d93">d0aa2263</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-11-16T20:06:25+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
<span class="new-file">
+
debian/patches/2to3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#b1dbf22e88351ec0d5d1d1a7f53295504b480e61">
<span class="new-file">
+
debian/salsa-ci.yml
</span>
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new new_line" 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="LC1" class="line" lang="plaintext">dindel (1.01-wu1-3+dfsg-2) unstable; urgency=medium</span>
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<td class="diff-line-num new new_line" 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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Standards-Version: 4.5.0 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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"> * Remove trailing whitespace in debian/rules (routine-update)</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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"> * Add salsa-ci file (routine-update)</span>
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<td class="diff-line-num new new_line" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num new new_line" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove obsolete field Name from debian/upstream/metadata (already present in</span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> machine-readable debian/copyright).</span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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"> * watch file standard 4 (routine-update)</span>
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<td class="diff-line-num new new_line" 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"> * d/rules: Remove boilerplate</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> * Call 2to3 on Python scripts</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 16 Nov 2020 20:03:42 +0100</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">dindel (1.01-wu1-3+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#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">@@ -5,16 +5,17 @@ Uploaders: Animesh Sharma <sharma.animesh@gmail.com>,</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> seqan-dev<span class="idiff left right"> (>= 1.4.1)</span>,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 13</span>),</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> seqan-dev,</span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libbam-dev,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libboost-program-options-dev,</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libboost-math-dev,</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> zlib1g-dev</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</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">5</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/dindel</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/dindel.git</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext">Homepage: https://github.com/genome/dindel-tgi</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: dindel</span>
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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/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#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">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 16 Nov 2020 19:27:15 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Call 2to3 on Python scripts</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">diff --git a/python/convertVCFToDindel.py b/python/convertVCFToDindel.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">index e8efde8..546138b 100644</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/convertVCFToDindel.py</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/convertVCFToDindel.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import os, sys, glob, gzip, math</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> from optparse import OptionParser</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> # Make sure to set the proper PYTHONPATH before running this script:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/makeGenotypeLikelihoodFilePooled.py b/python/makeGenotypeLikelihoodFilePooled.py</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">index effcdd0..880b490 100644</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/makeGenotypeLikelihoodFilePooled.py</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/makeGenotypeLikelihoodFilePooled.py</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -31,18 +31,18 @@</span> def getCalls(callFile = ''):</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> newpos = pos + var.offset - 1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> newstr = var.str</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not calls.has_key(chrom):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chrom not in calls:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> calls[chrom] = {}</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not calls[chrom].has_key(newpos):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if newpos not in calls[chrom]:</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> calls[chrom][newpos] = {}</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if calls[chrom][newpos].has_key(newstr):</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if newstr in calls[chrom][newpos]:</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> raise NameError('Multiple same variants?')</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> calls[chrom][newpos][newstr] = dat.copy()</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> numcalls += 1</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> vcf.close()</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Number of calls imported:",numcalls</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Number of calls imported:",numcalls)</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> return calls</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -126,7 +126,7 @@</span> def loadGLFFiles(inputGLFFiles = ''):</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> dat = fg.readline()</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> if dat['realigned_position'] != 'NA':</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> firstpos = int(dat['realigned_position'])</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if fp_to_fname.has_key(firstpos):</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if firstpos in fp_to_fname:</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> raise NameError('Huh?')</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> fp_to_fname[firstpos] = glffile</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="p">@@ -135,7 +135,7 @@</span> def loadGLFFiles(inputGLFFiles = ''):</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> newglffiles = []</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> for pos in sorted(fp_to_fname.keys()):</span>
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<td class="diff-line-num new new_line" data-linenumber="55" 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">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "pos:",pos,"glffile:", fp_to_fname[pos]</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("pos:",pos,"glffile:", fp_to_fname[pos])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> newglffiles.append(fp_to_fname[pos])</span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> return newglffiles</span>
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<td class="diff-line-num new new_line" data-linenumber="60" 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">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -185,7 +185,7 @@</span> def makeGLF(inputGLFFiles = '', outputFile = '', callFile = '', bamfilesFile = '</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> break</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> newindex = "%s.%s.%s" % (dat['index'], dat['realigned_position'], dat['nref_all'])</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not buffer.has_key(newindex):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if newindex not in buffer:</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> buffer[newindex] = []</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> buffer[newindex].append(dat)</span>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="p">@@ -205,7 +205,7 @@</span> def makeGLF(inputGLFFiles = '', outputFile = '', callFile = '', bamfilesFile = '</span>
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<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> fg.close()</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Number written:", numwritten</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Number written:", numwritten)</span></span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> sys.stdout.flush()</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> # finish up</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/makeWindows.py b/python/makeWindows.py</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gh" style="color: #999;">index 47c1bcf..be327bb 100644</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/makeWindows.py</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/makeWindows.py</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> from optparse import OptionParser</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> import sys, os, getopt</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -80,7 +80,7 @@</span> def write_output_candidates(newVariants, outputPrefix = '', variantsPerFile = 10</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> # results should be joined at the mergeOutput stage</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> </span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> windows.append(wsize)</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not histWindows.has_key(wsize):</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if wsize not in histWindows:</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> histWindows[wsize] = 1</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> else:</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> histWindows[wsize] += 1</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -117,8 +117,8 @@</span> def write_output_candidates(newVariants, outputPrefix = '', variantsPerFile = 10</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> sys.stderr.write("Mean window size: %d\n" % (sum(windows)/len(windows)))</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> if False:</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> for ws in sorted(histWindows.keys()):</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print " %d:%d" % (ws, histWindows[ws]),</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "\n"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(" %d:%d" % (ws, histWindows[ws]), end=' ')</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("\n")</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </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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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="p">@@ -140,7 +140,7 @@</span> def split_and_merge(inputVarFile = '', windowFilePrefix = '', minDist = 10, vari</span>
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<td class="diff-line-num new new_line" data-linenumber="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> pos = int(dat[1])</span>
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<td class="diff-line-num new new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> numread += 1</span>
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<td class="diff-line-num new new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> if numread % 10000 == 1:</span>
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<td class="diff-line-num new new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print numread,"lines read"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(numread,"lines read")</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> try:</span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> chrno = int(chr)</span>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> if chrno>24 or chrno == 0:</span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="p">@@ -148,10 +148,10 @@</span> def split_and_merge(inputVarFile = '', windowFilePrefix = '', minDist = 10, vari</span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> except ValueError:</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> pass</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not variants.has_key(chr):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chr not in variants:</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> variants[chr] = {}</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not variants[chr].has_key(pos):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if pos not in variants[chr]:</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> variants[chr][pos] = []</span>
</pre>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> i = 2 </span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="p">@@ -165,14 +165,14 @@</span> def split_and_merge(inputVarFile = '', windowFilePrefix = '', minDist = 10, vari</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> # output statistics</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> sys.stderr.write("Number of chromosomes: %d\n" % (len(variants)))</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;">- for chr in variants.keys():</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;">+ for chr in list(variants.keys()):</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> sys.stderr.write("\tchr %s: %d\n" % ( chr, len(variants[chr]) ))</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> # per chromosome: group variants and split</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> newVariants = {}</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> startIdx = 0</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for chr in variants.keys():</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for chr in list(variants.keys()):</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> totVar = 0</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> positions = sorted(variants[chr].keys())</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> newPosition = positions[:]</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="p">@@ -191,7 +191,7 @@</span> def split_and_merge(inputVarFile = '', windowFilePrefix = '', minDist = 10, vari</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> newPos = newPosition[p]</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> pos = positions[p]</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> </span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not newVariants[chr].has_key(newPos):</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if newPos not in newVariants[chr]:</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> newVariants[chr][newPos] = []</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> for var in variants[chr][pos]:</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/mergeOutputDiploid.py b/python/mergeOutputDiploid.py</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gh" style="color: #999;">index aa46713..8d6c41f 100644</span></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;">--- a/python/mergeOutputDiploid.py</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;">+++ b/python/mergeOutputDiploid.py</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</span></span>
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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;">+#!/usr/bin/env python3</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> import os, sys, glob, gzip, math</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> from optparse import OptionParser</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> # Make sure to set the proper PYTHONPATH before running this script:</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span> def getPercentiles(hist = {}, pctiles = [ 1,5,10,25, 50, 75, 90, 95, 99]):</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> cum[k] += cum[prevk]</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> prevk = k</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> </span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not cum.has_key(0):</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if 0 not in cum:</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> cum[0] = 0</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> tot = cum[prevk]</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> iles = pctiles</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -227,10 +227,10 @@</span> def processDiploidGLFFile(glfFile = '', variants = {}, refFile = '', maxHPLen =</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> glf['genotype'] = dat['glf']</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> </span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> (vcf_str,report_pos) = getVCFString(glf = glf, fa = fa, filterQual = filterQual)</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not variants.has_key(chrom):</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chrom not in variants:</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> variants[chrom] = {}</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> </span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not variants[chrom].has_key(report_pos):</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if report_pos not in variants[chrom]:</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> variants[chrom][report_pos] = []</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> </span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> variants[chrom][report_pos].append(vcf_str)</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="p">@@ -305,12 +305,12 @@</span> def mergeOutput(glfFilesFile = '', sampleID = 'SAMPLE', refFile = '', maxHPLen =</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> processDiploidGLFFile(glfFile = gf, variants = variants, refFile = refFile, maxHPLen = maxHPLen, isHomozygous = isHomozygous, newVarCov = newVarCov, doNotFilterOnFR = doNotFilterOnFR, filterQual = filterQual)</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> </span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> this_chr = chromosomes[:]</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for chr in variants.keys():</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for chr in list(variants.keys()):</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> if chr not in this_chr:</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> this_chr.append(chr)</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> </span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> for chr in this_chr:</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if variants.has_key(chr):</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chr in variants:</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> for pos in sorted(variants[chr].keys()):</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> for vcfLine in variants[chr][pos]:</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> fv.write("%s\n" % (vcfLine))</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/mergeOutputPooled.py b/python/mergeOutputPooled.py</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gh" style="color: #999;">index a503ed3..e26b27b 100644</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/mergeOutputPooled.py</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/mergeOutputPooled.py</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> import os, sys, glob, gzip, math</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> from optparse import OptionParser</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> # Make sure to set the proper PYTHONPATH before running this script:</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span> def getPercentiles(hist = {}, pctiles = [ 1,5,10,25, 50, 75, 90, 95, 99]):</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> cum[k] += cum[prevk]</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> prevk = k</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not cum.has_key(0):</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if 0 not in cum:</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> cum[0] = 0</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> tot = cum[prevk]</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"> iles = pctiles</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> rdhist = {}</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> for glffile in allFiles:</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> fglf = FileUtils.FileWithHeader(fname = glffile, mode = 'r', joinChar = ' ')</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading", glffile</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading", glffile)</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> done = False</span>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> while True:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="230" 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">
230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> pos = -1</span>
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<td class="diff-line-num new new_line" data-linenumber="231" 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">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="p">@@ -289,7 +289,7 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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<td class="diff-line-num new new_line" data-linenumber="232" 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">
232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> nr += 1</span>
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<td class="diff-line-num new new_line" data-linenumber="233" 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">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> if nr % 10000 == 9999:</span>
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<td class="diff-line-num new new_line" data-linenumber="235" 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">
235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Number of lines read:",nr+1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Number of lines read:",nr+1)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="237" 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">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="238" 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">
238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> num_ind_with_data = 0</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" 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">
239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> tot_coverage = 0</span>
</pre>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="p">@@ -355,16 +355,16 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
</pre>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> prob = float(dat[col_post_prob])</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> freq = float(dat[headerLabels.index('est_freq')])</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if rdhist.has_key(tot_coverage):</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if tot_coverage in rdhist:</span></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> rdhist[tot_coverage] += 1</span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> else:</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> rdhist[tot_coverage] = 1</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> </span>
</pre>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> </span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> if prob>0.20:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not varStat.has_key(chr):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="253" 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">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chr not in varStat:</span></span>
</pre>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> varStat[chr] = {}</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not varStat[chr].has_key(pos):</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if pos not in varStat[chr]:</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> varStat[chr][pos] = {}</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> # hplen</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> seq = fa.get(chr, pos+1-25,50)</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="p">@@ -386,9 +386,9 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> fqp = 1.0 - math.pow(10.0, -float(filterQual)/10.0)</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> fqp_str = "q%d" % filterQual</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> </span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for chr in varStat.keys():</span></span>
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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;">- for pos in varStat[chr].keys():</span></span>
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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;">- for varseq, var in varStat[chr][pos].iteritems():</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for chr in list(varStat.keys()):</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for pos in list(varStat[chr].keys()):</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for varseq, var in varStat[chr][pos].items():</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> </span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> filters = [] </span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> prob = var['QUAL']</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="p">@@ -412,9 +412,9 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> filters.append("mf")</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> </span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> if filters == []:</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not pass_filters.has_key(chr):</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chr not in pass_filters:</span></span>
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<td class="diff-line-num new new_line" 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"> pass_filters[chr]={}</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not pass_filters[chr].has_key(pos):</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if pos not in pass_filters[chr]:</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> pass_filters[chr][pos]=[]</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> pass_filters[chr][pos].append(varseq)</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> num_pass += 1</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="p">@@ -433,7 +433,7 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"> chromosomes.extend(other_chr)</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"> </span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> # create VCF file</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Writing VCF"</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Writing VCF")</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> </span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> fv = open(outputVCFFile, 'w')</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> fv.write("##fileformat=VCFv4.0\n")</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="p">@@ -461,7 +461,7 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> </span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> </span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> for chr in chromosomes:</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not pass_filters.has_key(chr):</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chr not in pass_filters:</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> continue</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> # filter out variants that are too close</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> totSites = 0</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="p">@@ -481,23 +481,23 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> newPos = newPosition[p]</span>
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<td class="diff-line-num new new_line" data-linenumber="305" 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">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> pos = positions[p]</span>
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<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not newSites.has_key(newPos):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="308" 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">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if newPos not in newSites:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="309" 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">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> newSites[newPos] = {}</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="311" 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">
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;">- if not newSites[newPos].has_key(pos):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if pos not in newSites[newPos]:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> newSites[newPos][pos]=[]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for var in varStat[chr][pos].keys():</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for var in list(varStat[chr][pos].keys()):</span></span>
</pre>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> newSites[newPos][pos].append(var)</span>
</pre>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "New number of sites:", len(newSites.keys())</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="320" 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">
320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Number of sites filtered:",len(pass_filters[chr].keys())-len(newSites.keys())</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="321" 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">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("New number of sites:", len(list(newSites.keys())))</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="322" 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">
322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Number of sites filtered:",len(list(pass_filters[chr].keys()))-len(list(newSites.keys())))</span></span>
</pre>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> </span>
</pre>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> # select best call for double sites</span>
</pre>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> </span>
</pre>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> filtered = []</span>
</pre>
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<td class="diff-line-num new new_line" 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;">- for newPos in newSites.keys():</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" 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="gd" style="color: #000; background-color: #fdd;">- old = newSites[newPos].keys()</span></span>
</pre>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for newPos in list(newSites.keys()):</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ old = list(newSites[newPos].keys())</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> </span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> pos_probs = []</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> pos_vars = []</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="p">@@ -523,7 +523,7 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> filtered.append(pos_pos[idx])</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> </span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> for duppos in set(old)-set([okpos]):</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for var in varStat[chr][duppos].keys():</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for var in list(varStat[chr][duppos].keys()):</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> </span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> if varStat[chr][duppos][var]['filter'] == '':</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> varStat[chr][duppos][var]['filter'] == tcFilter</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="p">@@ -531,11 +531,11 @@</span> def processPooledGLFFiles(bamFilesFile = '', glfFilesFile = '', refFile = '', ou</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> varStat[chr][duppos][var]['filter']+=';'+tcFilter</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> </span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> </span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Number of indel sites:",len(filtered)</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Number of indel sites:",len(filtered))</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> </span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> </span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"> for pos in sorted(varStat[chr].keys()):</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for var in varStat[chr][pos].keys():</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for var in list(varStat[chr][pos].keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> indel_report_pos = pos</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/selectCandidates.py b/python/selectCandidates.py</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gh" style="color: #999;">index a11ca0d..53e297d 100644</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/selectCandidates.py</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/selectCandidates.py</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="p">@@ -1,11 +1,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> import os, sys, glob, gzip, math</span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> from optparse import OptionParser</span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> def emptyBuffer(fo = 0, variants = {}, parameters = {}, chrom = ''):</span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> for p in sorted(variants.keys()):</span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v in variants[p].keys():</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v in list(variants[p].keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> if variants[p][v]>=parameters['minCount'] and variants[p][v]<=parameters['maxCount']:</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> fo.write("%s %d %s # %d\n" % (chrom, p, v, variants[p][v]))</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span> def selectCandidates(inputFile = '', outputFile = '', parameters = {}):</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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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"> </span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> if chr != currChr:</span>
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<td class="diff-line-num new new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if visitedChromosomes.has_key(chr):</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if chr in visitedChromosomes:</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> raise NameError("Chromosome already processed. Please sort with respect to chromosome first and then position!")</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> currChr = chr</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> visitedChromosomes[chr]=1</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="p">@@ -56,7 +56,7 @@</span> def selectCandidates(inputFile = '', outputFile = '', parameters = {}):</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"> if pos == currPos:</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> for idx, v in enumerate(vars):</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;">- if not variants[pos].has_key(v):</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;">+ if v not in variants[pos]:</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> variants[pos][v]=0</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> variants[pos][v] += int(freqs[idx])</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> </span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/utils/Fasta.py b/python/utils/Fasta.py</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gh" style="color: #999;">index 6ed1f38..50ed185 100644</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/utils/Fasta.py</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/utils/Fasta.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="397" 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">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="p">@@ -36,7 +36,7 @@</span> class Fasta:</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> try:</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> idx = self.fai.ft[tid]</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> except KeyError:</span>
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<td class="diff-line-num new new_line" data-linenumber="401" 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">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'KeyError: ', tid</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('KeyError: ', tid)</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> raise NameError('KeyError')</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> fpos = idx.offset+ ( int(pos)/idx.blen)*idx.llen + (int(pos)%idx.blen)</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> self.fa.seek(fpos,0)</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="p">@@ -59,7 +59,7 @@</span> def getChromosomes(faFile = ''):</span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> </span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> faidx = FastaIndex(faiFile)</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> </span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fachr = faidx.ft.keys()</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fachr = list(faidx.ft.keys())</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> chromosomes = []</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> autosomal = ["%d" % c for c in range(1,23)]</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/utils/FileUtils.py b/python/utils/FileUtils.py</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gh" style="color: #999;">index ce15726..4e265cd 100644</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/utils/FileUtils.py</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/utils/FileUtils.py</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"><span class="p">@@ -93,7 +93,7 @@</span> class FileWithHeader:</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> raise NameError('File not opened for writing')</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> out = self.emptyline[:]</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for key,value in data.iteritems():</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for key,value in data.items():</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> if not key in self.lab_to_col:</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> self.nlabnotfound += 1</span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="p">@@ -195,15 +195,15 @@</span> def sortFile(fname = '', foutname='', col = 1, splitChar = ''):</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"> </span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> try: </span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> val = float(coldata[sortcol])</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if data.has_key(val):</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if val in data:</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> data[val].append(line)</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> else:</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> data[val]=[line]</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> except ValueError:</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print 'Columns contains non-numeric data'</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print('Columns contains non-numeric data')</span></span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> sys.exit(2)</span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> </span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keys = data.keys()</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ keys = list(data.keys())</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> keys.sort()</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"> for key in keys:</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/python/utils/VCFFile.py b/python/utils/VCFFile.py</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gh" style="color: #999;">index d95f622..4e32bb9 100644</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/python/utils/VCFFile.py</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/python/utils/VCFFile.py</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="p">@@ -21,18 +21,18 @@</span> class VCFFile:</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> self.f.write("##fileformat=VCF4\n")</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> </span>
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454
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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="LC454" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="455" 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">
455
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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="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for inf_id in info.keys():</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="456" 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">
456
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for inf_id in list(info.keys()):</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="457" 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">
457
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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="LC457" class="line" lang="diff"> line = "##INFO=<ID=%s,Number=%s,Type=%s,Description=\"%s\">" % (info[inf_id]['ID'], info[inf_id]['Number'], info[inf_id]['Type'], info[inf_id]['Description'])</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="458" 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">
458
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"> self.f.write(line+'\n')</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="459" 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">
459
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"> self.headerLines.append(line)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="460" 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">
460
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"> self.info[ info[inf_id]['ID'] ] = info[inf_id].copy()</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="461" 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">
461
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for id in filter.keys():</span></span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="462" 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">
462
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for id in list(filter.keys()):</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="463" 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">
463
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"> line = "##FILTER=<ID=%s,Description=\"%s\">" % (filter[id]['ID'],filter[id]['Description'])</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="464" 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">
464
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"> self.f.write(line+'\n')</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="465" 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">
465
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"> self.headerLines.append(line)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="466" 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">
466
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> self.filter[ filter[id]['ID'] ] = filter[id].copy()</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="467" 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">
467
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> </span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="468" 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">
468
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for id in format.keys():</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="469" 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">
469
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for id in list(format.keys()):</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="470" 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">
470
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"> line = "##FORMAT=<ID=%s,Number=%s,Type=%s,Description=\"%s\">" % (format[id]['ID'], format[id]['Number'], format[id]['Type'], format[id]['Description'])</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="471" 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">
471
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> self.f.write(line+'\n')</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="472" 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">
472
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> self.headerLines.append(line)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="473" 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">
473
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="p">@@ -130,7 +130,7 @@</span> class VCFFile:</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="474" 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">
474
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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="LC474" class="line" lang="diff"> type = fields2[2]</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="475" 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">
475
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"> description = fields1[-2]</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="476" 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">
476
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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="LC476" class="line" lang="diff"> </span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="477" 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">
477
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.info.has_key(id):</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="478" 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">
478
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if id in self.info:</span></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> raise NameError("VCF file already has info-id %s" % id)</span>
</pre>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"> </span>
</pre>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> self.info[id]= {'Number':number, 'ID':id, 'Type':type, 'Description':description}</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="482" 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">
482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="p">@@ -183,7 +183,7 @@</span> class VCFFile:</span>
</pre>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> </span>
</pre>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> description = fields1[-2]</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="486" 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">
486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.filter.has_key(id):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="487" 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">
487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if id in self.filter:</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> raise NameError("VCF file already has info-id %s" % id)</span>
</pre>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> </span>
</pre>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"> self.filter[id]= {'Number':number, 'ID':id, 'Type':type, 'Description':description.replace('"','')}</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="491" 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">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="p">@@ -226,7 +226,7 @@</span> class VCFFile:</span>
</pre>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> type = fields2[2]</span>
</pre>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> description = fields1[-2]</span>
</pre>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="495" 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">
495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if self.format.has_key(id):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="496" 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">
496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if id in self.format:</span></span>
</pre>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> raise NameError("VCF file already has info-id %s" % id)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="498" 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">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> </span>
</pre>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> self.format[id]= {'Number':number, 'ID':id, 'Type':type, 'Description':description.replace('"','')}</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="500" 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">
500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="p">@@ -323,7 +323,7 @@</span> class VCFFile:</span>
</pre>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> # output filters</span>
</pre>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> out['FILTER'] = col[ self.lab_to_col['FILTER'] ].split(';')</span>
</pre>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> </span>
</pre>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for filter in self.filter.keys():</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="505" 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">
505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for filter in list(self.filter.keys()):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="506" 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">
506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"> hs = "FILTER_%s" % filter</span>
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<td class="diff-line-num new new_line" data-linenumber="507" 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">
507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> if filter in out['FILTER']:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="508" 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">
508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> out[hs] = '1'</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="509" 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">
509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="p">@@ -357,7 +357,7 @@</span> class VCFFile:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="510" 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">
510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> raise NameError("Can only write in write-mode")</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="511" 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">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> linedata = []</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="512" 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">
512
</td>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> for lab in self.headerLabels:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="513" 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">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not dat.has_key(lab):</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="514" 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">
514
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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="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if lab not in dat:</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="515" 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">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> raise NameError("Cannot find label %s in input" % lab)</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="516" 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">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="517" 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">
517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> for lab in ['CHROM','POS','ID', 'REF','ALT','QUAL']:</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="518" 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">
518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="p">@@ -375,15 +375,15 @@</span> class VCFFile:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="519" 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">
519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> else:</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="520" 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">
520
</td>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> if checkTags:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="521" 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">
521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> for fi in dat['FILTER']:</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="522" 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">
522
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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="LC522" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not self.filter.has_key(fi):</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="523" 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">
523
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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="LC523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if fi not in self.filter:</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="524" 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">
524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> raise NameError('Undefined filter!')</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="525" 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">
525
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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="LC525" class="line" lang="diff"> linedata.append(';'.join(dat['FILTER']))</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="526" 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">
526
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="527" 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">
527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> # info</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="528" 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">
528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"> infos = []</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="529" 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">
529
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for inf in dat['INFO'].keys():</span></span>
</pre>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for inf in list(dat['INFO'].keys()):</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> if checkTags:</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if not self.info.has_key(inf):</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if inf not in self.info:</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> raise NameError('Undefined info tag!')</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> if self.info[inf]['Type'] == 'Flag':</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> infos.append(inf)</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">modernize-Makefile.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">compiler_errors.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">fix-ftbfs-with-gcc6.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,4 +4,4 @@</td>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_BUILD_MAINT_OPTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all</span>
</pre>
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5
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"></span>
</pre>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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7
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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span><span class="idiff left right"> </span></span></pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"> dh <span class="nv" style="color: #008080;">$@</span></span></pre>
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<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#b1dbf22e88351ec0d5d1d1a7f53295504b480e61"><strong>debian/salsa-ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="nn" style="color: #555;">---</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml</span></span></pre>
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<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Contact: Cornelis A. Albers</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Name: dindel</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> Author: ></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Cornelis A. Albers and Gerton Lunter and Daniel G. MacArthur and</span>
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<a href="https://salsa.debian.org/med-team/dindel/-/compare/13f18fb8027692eaceaae6f3b07afbcd53ad3f61...d0aa2263b255d495f3598b1e0366cccbeb7b7d93#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">version=<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> https://github.com/genome/dindel-tgi/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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