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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/strelka">Debian Med / strelka</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/strelka/-/commit/716b7fc26e889616e0a58c850c2271d31e9edef8">716b7fc2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T10:52:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enable cmake configuring
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/strelka/-/commit/7fbdd9e5cf6633fe93e43b3e7e8e753a3a5a30f3">7fbdd9e5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-14T11:07:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Weak and totally untested attempt to port to Python3 by using 2to3
</pre>
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<h4>4 changed files:</h4>
<ul>
<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">
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+
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/strelka/-/compare/8f85277cf3b3cb42417a2bd3fad7748f39f45b63...7fbdd9e5cf6633fe93e43b3e7e8e753a3a5a30f3#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" 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">@@ -6,7 +6,16 @@ Priority: optional</td>
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> python3</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"> python3,</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"> libboost-date-time-dev,</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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> libboost-filesystem-dev,</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">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libboost-program-options-dev,</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"> libboost-serialization-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> libboost-system-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(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="LC15" class="line" lang="plaintext"> libboost-timer-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="plaintext"> libboost-chrono-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(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="LC17" class="line" lang="plaintext"> libboost-test-dev,</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="plaintext"> zlib1g-dev</span>
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="20" 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="LC20" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/strelka</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/strelka.git</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/strelka/-/compare/8f85277cf3b3cb42417a2bd3fad7748f39f45b63...7fbdd9e5cf6633fe93e43b3e7e8e753a3a5a30f3#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: Wed, 13 May 2020 16:55:22 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Weak and totally untested attempt to port to Python3 by using 2to3</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/CMakeLists.txt</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -125,15 +125,15 @@</span> set(THIS_PROJECT_NAME "strelka")</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> project (${THIS_PROJECT_NAME})</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# Find python2 interpreter</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-find_package(PythonInterp 2 QUIET)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# Find python3 interpreter</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+find_package(PythonInterp 3 QUIET)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> if (NOT PYTHONINTERP_FOUND)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- message (WARNING "No python2 interpreter found, disabling optional python build and installation components. Installed workflow requires python2 interpreter to run.")</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ message (WARNING "No python3 interpreter found, disabling optional python build and installation components. Installed workflow requires python3 interpreter to run.")</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> else()</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- set (MINIMUM_PYTHON_VERSION "2.6")</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set (MINIMUM_PYTHON_VERSION "3.6")</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> if (${PYTHON_VERSION_STRING} VERSION_LESS ${MINIMUM_PYTHON_VERSION})</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> message (WARNING</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "Python2 interpretor must be at least version (${MINIMUM_PYTHON_VERSION}). Found version ${PYTHON_VERSION_STRING} at '${PYTHON_EXECUTABLE}'."</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;">+ "Python3 interpretor must be at least version (${MINIMUM_PYTHON_VERSION}). Found version ${PYTHON_VERSION_STRING} at '${PYTHON_EXECUTABLE}'."</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> " Disabling optional python build and installation components. Installed workflow requires python ${MINIMUM_PYTHON_VERSION} or higher to run.")</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> set(PYTHONINTERP_FOUND false)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> endif ()</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/docs/developerGuide/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/docs/developerGuide/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -191,7 +191,7 @@</span> see the `builderImage` variable.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> ## Coding Guidelines</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Supported project languages are C++11 for core methods development and python2 (2.6+) for workflow and scripting support.</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Supported project languages are C++11 for core methods development and python3 (3.6+) for workflow and scripting support.</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> ### Source formatting</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/config/validate/validateJsonModelFromSchema.py</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/config/validate/validateJsonModelFromSchema.py</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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="LC44" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/bin/configureStrelkaGermlineWorkflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/bin/configureStrelkaGermlineWorkflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC51" 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="LC52" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -24,13 +24,9 @@</span> This script configures the strelka germl</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> import os,sys</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info >= (3,0):</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if sys.version_info < (3,6):</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> import platform</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception("Strelka does not currently support python3 (version %s detected)" % (platform.python_version()))</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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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 sys.version_info < (2,6):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import platform</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception("Strelka requires python2 version 2.6+ (version %s detected)" % (platform.python_version()))</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise Exception("Strelka requires python3 version 3.6+ (version %s detected)" % (platform.python_version()))</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> scriptDir=os.path.abspath(os.path.dirname(__file__))</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/bin/configureStrelkaSomaticWorkflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/bin/configureStrelkaSomaticWorkflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -24,13 +24,9 @@</span> This script configures the Strelka somat</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> import os,sys</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info >= (3,0):</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if sys.version_info < (3,6):</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> import platform</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception("Strelka does not currently support python3 (version %s detected)" % (platform.python_version()))</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info < (2,6):</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import platform</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception("Strelka requires python2 version 2.6+ (version %s detected)" % (platform.python_version()))</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise Exception("Strelka requires python3 version 3.6+ (version %s detected)" % (platform.python_version()))</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> scriptDir=os.path.abspath(os.path.dirname(__file__))</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/deNovoQualityScore/denovo.py</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/deNovoQualityScore/denovo.py</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC99" 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="LC100" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> #</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> import argparse</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> import csv</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="p">@@ -206,7 +206,7 @@</span> def check_pedigree_input(pedigree, sampl</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> raise ValueError(msg)</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> # check if all pedigree sample names are referenced in the header</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k, v in pedigree.iteritems():</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k, v in pedigree.items():</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> if v not in samples:</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> msg = "Sample '{1}' for {0} missing in the input VCF.".format(k, v)</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> raise ValueError(msg)</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="p">@@ -372,8 +372,8 @@</span> def full_genotype_mapping(gtsu_idx):</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> """Map trio sample genotypes to DNG indexing schema"""</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> n = len(gtsu_idx)</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- full_idx = itertools.product(xrange(n), xrange(n), xrange(n))</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- idx_gtsu = {v: k for k, v in gtsu_idx.iteritems()} # index->GT mapping</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ full_idx = itertools.product(range(n), range(n), range(n))</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ idx_gtsu = {v: k for k, v in gtsu_idx.items()} # index->GT mapping</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> full_gt = [</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> "/".join([paste(idx_gtsu[k]), paste(idx_gtsu[j]), paste(idx_gtsu[i])])</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> for i, j, k in full_idx</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="p">@@ -475,7 +475,7 @@</span> def read_prior(path, vartype):</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> 'names': col_names,</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> 'formats': col_formats</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> })</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- prior = dict(zip(col_names, prior))</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prior = dict(list(zip(col_names, prior)))</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> prior['denovo_flag'].astype(bool)</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> </span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -503,10 +503,10 @@</span> def reorder_prior(prior, full_gt_idx):</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> """Reorder imported prior to match the DNG genotype order"""</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> p_gt = {g: i for i, g in enumerate(prior['gt'])}</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- idx_full_gt = {v: k for k, v in full_gt_idx.iteritems()} # revert mapping</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- new_prior_ord = [p_gt[idx_full_gt[i]] for i in xrange(len(idx_full_gt))]</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ idx_full_gt = {v: k for k, v in full_gt_idx.items()} # revert mapping</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ new_prior_ord = [p_gt[idx_full_gt[i]] for i in range(len(idx_full_gt))]</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- prior = {k: np.take(v, new_prior_ord, axis=0) for k, v in prior.iteritems()}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ prior = {k: np.take(v, new_prior_ord, axis=0) for k, v in prior.items()}</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> return prior</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"><span class="p">@@ -542,7 +542,7 @@</span> def allele_indices(alleles, genotype_ind</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> """Return ordered indices for allele combinations for PL field"""</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> </span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> indices = [genotype_index[alleles[j], alleles[i]]</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(len(alleles)) for j in xrange(i + 1)]</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(len(alleles)) for j in range(i + 1)]</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> return indices</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> </span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="p">@@ -558,9 +558,9 @@</span> def build_PL_indices_lookup(alleles, gen</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> alleles, repeat=3),</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> itertools.product(</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> alleles, repeat=4))</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alleles_comb = itertools.ifilter(</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alleles_comb = filter(</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> lambda x: len(set(x)) == min(len(x), n_uniq_alleles), alleles_comb)</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alleles_comb = itertools.ifilter(lambda x: ref not in x[1:], alleles_comb)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alleles_comb = filter(lambda x: ref not in x[1:], alleles_comb)</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> alleles_lookup = {</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> alleles: allele_indices(alleles, genotype_index)</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> for alleles in alleles_comb</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="p">@@ -800,7 +800,7 @@</span> def calculate_dng_DQ_indel(variant, prio</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"> try:</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> pl = get_PL_field(variant)</span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alleles = tuple(['R'] + ['V' for i in xrange(len(variant.ALT))])</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alleles = tuple(['R'] + ['V' for i in range(len(variant.ALT))])</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> alleles_idx = get_PL_indices_indel(alleles)</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> C = map_sample_pl_indel(pl[sample_index[0]], alleles_idx)</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> M = map_sample_pl_indel(pl[sample_index[1]], alleles_idx)</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="p">@@ -846,7 +846,7 @@</span> def calculate_dng_DQ_sv(variant, prior,</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"> try:</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> pl = get_PL_field(variant)</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alleles = tuple(['R'] + ['V' for i in xrange(len(variant.ALT))])</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ alleles = tuple(['R'] + ['V' for i in range(len(variant.ALT))])</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> alleles_idx = get_PL_indices_indel(alleles)</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> C = map_sample_pl_indel(pl[sample_index[0]], alleles_idx)</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> M = map_sample_pl_indel(pl[sample_index[1]], alleles_idx)</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="p">@@ -897,7 +897,7 @@</span> def add_DQ_score_to_variant(variant, par</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> # if variant has no DQ format field yet</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> # append the DQ score to the proband and 'missing' to all other samples</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> fields[8] += ':' + _field_name</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;">- for i in xrange(param['n_samples']):</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;">+ for i in range(param['n_samples']):</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> field_value, field_index = \</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> select_sample_score(score, i, sample_index_child, decimals, null_value)</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> fields[field_index] = fields[field_index] + ':' + field_value</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="p">@@ -1011,7 +1011,7 @@</span> def import_bed_regions(path, fieldnames=</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> coords = (int(entry['start']), int(entry['end']))</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> regions.setdefault(contig, list()).append(coords)</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> # convert values from list to tuple</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- regions = {contig: tuple(coords) for contig, coords in regions.iteritems()}</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ regions = {contig: tuple(coords) for contig, coords in regions.items()}</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> except (IOError, BaseException):</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> regions = None</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="p">@@ -1067,7 +1067,7 @@</span> if __name__ == '__main__':</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> parser.add_argument(</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> '--model',</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> required=False,</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- choices=_models.keys(),</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ choices=list(_models.keys()),</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> default=_default_model_name,</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> help=argparse.SUPPRESS)</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/deNovoQualityScore/test/test</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/deNovoQualityScore/test/test</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="p">@@ -8,4 +8,4 @@</span> test_dir=$( cd "$(dirname "${BASH_SOURCE</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> base_dir=$( dirname ${test_dir} )</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> # Run the tests without changing the current directory</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-( cd ${base_dir} && python2 -m pytest "$@" )</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+( cd ${base_dir} && python3 -m pytest "$@" )</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/deNovoQualityScore/test/test_denovo.py</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/deNovoQualityScore/test/test_denovo.py</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC233" 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="LC234" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="p">@@ -101,7 +101,7 @@</span> def datasets():</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> 'par_bed': 'PARv5.bed'</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- paths = {name: get_test_data_path(path) for name, path in files.iteritems()}</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ paths = {name: get_test_data_path(path) for name, path in files.items()}</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> return paths</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="p">@@ -284,7 +284,7 @@</span> def test_cmd_ids_spw_ref(datasets, tempd</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> n_hit = 0</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"> n_called = {'indel': 0, 'snp': 0}</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for variant, variant2 in itertools.izip(vr1, vr2):</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for variant, variant2 in zip(vr1, vr2):</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> assert variant == variant2</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> for sample in variant.samples:</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> assert 'DQ' in sample.data._fields</span>
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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="p">@@ -340,7 +340,7 @@</span> def test_cmd_parallel_spw_ref(datasets,</span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> n_hit = 0</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> n_called = {'indel': 0, 'snp': 0}</span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for variant, variant2 in itertools.izip(vr1, vr2):</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for variant, variant2 in zip(vr1, vr2):</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> assert variant == variant2</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> for sample in variant.samples:</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> assert 'DQ' in sample.data._fields</span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="p">@@ -398,7 +398,7 @@</span> def test_cmd_single_parallel_spw_compari</span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> assert vr1.metadata['denovo_program'][0] == vr2.metadata['denovo_program'][0]</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> assert vr1.formats['DQ'] == vr1.formats['DQ']</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> </span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for variant, variant2 in itertools.izip(vr1, vr2):</span></span>
</pre>
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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 variant, variant2 in zip(vr1, vr2):</span></span>
</pre>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> assert variant == variant2</span>
</pre>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> </span>
</pre>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> </span>
</pre>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="p">@@ -494,7 +494,7 @@</span> def test_cmd_pedphase_filter_spw(dataset</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> check_denovo_header(vr2)</span>
</pre>
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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"> n_denovo = n_no_denovo = n_no_dq = 0</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;">- for variant, variant2 in itertools.izip(vr1, vr2):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for variant, variant2 in zip(vr1, vr2):</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"> assert variant == variant2</span>
</pre>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> # compare against simulation tags</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> has_dq_field = 'DQ' in variant.samples[0].data._fields</span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="p">@@ -566,7 +566,7 @@</span> def test_cmd_proband_sibling_five_sample</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> sample_indices = lambda vcf, samples: \</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> [vcf.samples.index(sample) for sample in samples]</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for variant1, variant2 in itertools.izip(vf1, vf2):</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for variant1, variant2 in zip(vf1, vf2):</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> # compare common most fields are the same</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> for field in ('CHROM', 'POS', 'ID', 'REF', 'ALT', 'FILTER', 'INFO', 'FORMAT'):</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> assert variant1.__getattribute__(field) == variant2.__getattribute__(field)</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="p">@@ -936,7 +936,7 @@</span> def test_python_spw_ref_five_samples(dat</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> assert variant.samples[child_idx]['DQ'] >= 20.0</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> n_hit += 1</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> if 'DQ' in variant.samples[child_idx].data._fields:</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for sample_index in xrange(len(variant.samples)):</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for sample_index in range(len(variant.samples)):</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> sample = variant.samples[sample_index]</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> if sample_index != child_idx:</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"> assert sample['DQ'] is None</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="p">@@ -991,7 +991,7 @@</span> def test_python_spw_old_prior_cases(data</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> def test_snv_prior_import_order():</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> """Test SNV prior import and reordering"""</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for prior_type, prior_path in denovo._prior_paths.iteritems():</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for prior_type, prior_path in denovo._prior_paths.items():</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> </span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> prior_path = prior_path['snv']</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> assert os.path.exists(prior_path)</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"><span class="p">@@ -1021,7 +1021,7 @@</span> def test_indel_length_prior_computation(</span>
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<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> assert len(mut_rate) == max_len+1</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"> assert np.all(np.diff(mut_rate) < 0.0) # decaying values</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> </span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for prior_type, prior_path in denovo._prior_paths.iteritems():</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for prior_type, prior_path in denovo._prior_paths.items():</span></span>
</pre>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> </span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> prior_path = prior_path['indel']</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> assert os.path.exists(prior_path)</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="p">@@ -1441,7 +1441,7 @@</span> def test_import_par_bed(datasets):</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> par = denovo.import_bed_regions(par_path)</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> </span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> # check properties of data structure</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for contig, coords in par.iteritems():</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for contig, coords in par.items():</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> assert contig == 'X'</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"> assert isinstance(coords, tuple)</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> for pos in coords:</span>
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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;">--- a/src/python/lib/checkChromSet.py</span></span>
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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="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/lib/checkChromSet.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="p">@@ -172,7 +172,7 @@</span> def checkChromSet(htsfileBin,referenceFa</span>
</pre>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> # first bam is used as a reference:</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> chromInfo = getBamChromInfo(htsfileBin,bamList[0])</span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- chroms = sorted(chromInfo.keys(),key=lambda x:chromInfo[x][1])</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ chroms = sorted(list(chromInfo.keys()),key=lambda x:chromInfo[x][1])</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> # check that first bam is compatible with reference:</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> for chrom in chroms :</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="p">@@ -184,7 +184,7 @@</span> def checkChromSet(htsfileBin,referenceFa</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> # optionally check that BAM contains all chromosomes in reference:</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> if isReferenceLocked :</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for refChrom in refChromInfo.keys() :</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for refChrom in list(refChromInfo.keys()) :</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> if refChrom not in chroms :</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> chromError("Reference genome mismatch: %s BAM/CRAM file is missing a chromosome found in the reference fasta file: '%s'" % (bamLabel[0], refChrom))</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="p">@@ -207,5 +207,5 @@</span> def checkChromSet(htsfileBin,referenceFa</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> # If all chromosomes matched, then compareChromInfo should be empty at this point.</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> # Check that no chromosomes are unique to the 'compare' BAM file.</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for chrom in compareChromInfo.keys() :</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for chrom in list(compareChromInfo.keys()) :</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> chromError("Reference genome mismatch: %s BAM/CRAM file is missing a chromosome found in the %s BAM/CRAM file: '%s'" % (bamLabel[0], bamLabel[index], chrom))</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/lib/configureOptions.py</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/lib/configureOptions.py</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="p">@@ -95,9 +95,9 @@</span> class ConfigureWorkflowOptions(object) :</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"> """</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> </span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> def updateIniSections(data,newData) :</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k in newData.keys() :</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k in list(newData.keys()) :</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> if k not in data : data[k] = {}</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for kk in newData[k].keys() :</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for kk in list(newData[k].keys()) :</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> data[k][kk] = newData[k][kk]</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> </span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> </span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="p">@@ -153,7 +153,7 @@</span> class ConfigureWorkflowOptions(object) :</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> </span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> # write options object back into full iniSections object:</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> #</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k,v in vars(options).iteritems() :</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k,v in vars(options).items() :</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> if k == "isAllHelp" : continue</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> iniSections[primary_section][k] = v</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 class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/lib/configureUtil.py</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/lib/configureUtil.py</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="p">@@ -41,7 +41,7 @@</span> def argToBool(x) :</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> class FalseStrings :</span>
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<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"> val = ("", "0", "false", "f", "no", "n", "off")</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> </span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if isinstance(x, basestring) :</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if isinstance(x, str) :</span></span>
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> return (x.lower() not in FalseStrings.val)</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> return bool(x)</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> </span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="p">@@ -88,7 +88,7 @@</span> def getPrimarySectionOptions(configSecti</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> </span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> options=WorkflowOptions()</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> if primarySection not in configSections : return options</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (k,v) in configSections[primarySection].items() :</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (k,v) in list(configSections[primarySection].items()) :</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> setattr(options,k,v)</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"> </span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> return options</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="p">@@ -112,7 +112,7 @@</span> def dumpIniSections(iniFile,iniSections)</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> """</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"> convert iniSections object, expected to be a hash or hashes, into an iniFile</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> """</span>
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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;">- from ConfigParser import SafeConfigParser</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;">+ from configparser import SafeConfigParser</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"> </span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> config = SafeConfigParser()</span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> config.optionxform=str</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="p">@@ -121,9 +121,9 @@</span> def dumpIniSections(iniFile,iniSections)</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"> if v is None : return ""</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> else : return str(v)</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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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for section in iniSections.keys():</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for section in list(iniSections.keys()):</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"> config.add_section(section)</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k,v in iniSections[section].items() :</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k,v in list(iniSections[section].items()) :</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> config.set(section,k,clean_value(v))</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"> configfp=open(iniFile,"w")</span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="p">@@ -136,7 +136,7 @@</span> def getIniSections(iniFile) :</span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"> parse the ini iniFile and return a hash of hashes</span>
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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"><span class="gd" style="color: #000; background-color: #fdd;">- from ConfigParser import SafeConfigParser</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from configparser import SafeConfigParser</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"> if not os.path.isfile(iniFile) : return {}</span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/lib/makeRunScript.py</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/lib/makeRunScript.py</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="p">@@ -60,7 +60,7 @@</span> def makeRunScript(scriptFile, workflowMo</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> sfp=open(scriptFile,"w")</span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> </span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> if pythonBin is None :</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pythonBin="/usr/bin/env python2"</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pythonBin="/usr/bin/env python3"</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> </span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> sfp.write(runScript1 % (pythonBin, " ".join(sys.argv),workflowModuleDir,workflowModuleName,workflowClassName))</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"> </span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span> def makeRunScript(scriptFile, workflowMo</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"> sfp.write('main(r"%s","%s",%s)\n' % (pickleConfigFile, primaryConfigSection, workflowClassName))</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"> sfp.write('\n')</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"> sfp.close()</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;">- os.chmod(scriptFile,0755)</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;">+ os.chmod(scriptFile,0o755)</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"> </span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="p">@@ -83,13 +83,9 @@</span> runScript1="""#!%s</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"> import os, sys</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"> </span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info >= (3,0):</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if sys.version_info < (3,6):</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> import platform</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception("Strelka does not currently support python3 (version %%s detected)" %% (platform.python_version()))</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info < (2,6):</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import platform</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception("Strelka requires python2 version 2.6+ (version %%s detected)" %% (platform.python_version()))</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise Exception("Strelka requires python3 version 3.6+ (version %%s detected)" %% (platform.python_version()))</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"> </span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> scriptDir=os.path.abspath(os.path.dirname(__file__))</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"> sys.path.append(r'%s')</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/lib/sharedWorkflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/lib/sharedWorkflow.py</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span> from workflowUtil import isWindows, preJ</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"> </span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"> </span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> def isString(x):</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return isinstance(x, basestring)</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return isinstance(x, str)</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"> def isIterable(x):</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/lib/strelkaSharedOptions.py</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/lib/strelkaSharedOptions.py</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span> def cleanLocals(locals_dict) :</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> When passed a locals() dictionary, clean out all of the hidden keys and return</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"> """</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"> </span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return dict((k,v) for (k,v) in locals_dict.items() if not k.startswith("__") and k != "self")</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return dict((k,v) for (k,v) in list(locals_dict.items()) if not k.startswith("__") and k != "self")</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"> </span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"> </span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> </span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="p">@@ -219,7 +219,7 @@</span> class StrelkaSharedWorkflowOptionsBase(C</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> (_, chromSizes) = getFastaChromOrderSize(referenceFastaIndex)</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> </span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> totalEstimationSize=0</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for chromSize in chromSizes.values() :</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for chromSize in list(chromSizes.values()) :</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"> if chromSize < Constants.minChromSize : continue</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> totalEstimationSize += chromSize</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> </span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/lib/workflowUtil.py</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/lib/workflowUtil.py</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="p">@@ -210,7 +210,7 @@</span> def getChromIntervals(chromOrder, chromS</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> segmentBaseSize=chromSize/chromSegments</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> nPlusOne=chromSize%chromSegments</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> start=chromStart</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(chromSegments) :</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(chromSegments) :</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> segSize=segmentBaseSize</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> if i<nPlusOne : segSize += 1</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> end=min(start+(segSize-1),chromStart+chromSize)</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/libexec/cat.py</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/cat.py</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> #</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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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;">--- a/src/python/libexec/configureSequenceAlleleCountsWorkflow.py</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/configureSequenceAlleleCountsWorkflow.py</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> #</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="p">@@ -24,13 +24,9 @@</span> This script configures the sequence erro</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> </span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> import os,sys</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"> </span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info >= (3,0):</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if sys.version_info < (3,6):</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"> import platform</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception("Strelka does not currently support python3 (version %s detected)" % (platform.python_version()))</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info < (2,6):</span></span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import platform</span></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;">- raise Exception("Strelka requires python2 version 2.6+ (version %s detected)" % (platform.python_version()))</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;">+ raise Exception("Strelka requires python3 version 3.6+ (version %s detected)" % (platform.python_version()))</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"> </span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"> </span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"> scriptDir=os.path.abspath(os.path.dirname(__file__))</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/libexec/configureStrelkaNoiseWorkflow.py</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/configureStrelkaNoiseWorkflow.py</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="p">@@ -89,9 +89,9 @@</span> You must specify a BAM or CRAM file.</span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> def main() :</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (sys.version_info[0] != 2):</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (sys.version_info[0] != 3):</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"> notefp=sys.stdout</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- notefp.write("""Failed to create workflow run script.\nPyflow only supports python2. Detected python %s on the system.\n""" % sys.version_info[0])</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ notefp.write("""Failed to create workflow run script.\nPython2 is End Of Life. Detected python %s on the system.\n""" % sys.version_info[0])</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"> return</span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> primarySectionName="snoise"</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/libexec/extractSmallIndelCandidates.py</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/extractSmallIndelCandidates.py</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"> #</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/libexec/mergeChromDepth.py</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/mergeChromDepth.py</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> #</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/libexec/sortVcf.py</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/sortVcf.py</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> #</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/libexec/updateNoPassedVariantGTsFilter.py</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/updateNoPassedVariantGTsFilter.py</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> #</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/libexec/vcfCmdlineSwapper.py</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/libexec/vcfCmdlineSwapper.py</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"> #</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/bin/evs_evaluate.py</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/bin/evs_evaluate.py</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"> #</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span> def parseArgs():</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"> parser.add_argument("-c", "--classifier", required=True,</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"> help="Classifier pickle file name")</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> parser.add_argument("-f", "--features",</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- choices=evs.features.FeatureSet.sets.keys(),</span></span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ choices=list(evs.features.FeatureSet.sets.keys()),</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"> required=True,</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"> help="Which feature set to use (or a comma-separated list of feature names,"</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"> " e.g. -f QSS_NT,T_DP_RATE")</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span> def main():</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"> datasets = []</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"> for i in args.inputs:</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> i = os.path.abspath(i)</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"> df = pandas.read_csv(i, na_values=".")</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> df.fillna("0", inplace=True)</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"> datasets.append(df)</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="p">@@ -115,7 +115,7 @@</span> def main():</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"> </span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"> result = pandas.concat(rlist)</span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> </span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print pandas.crosstab(result['tag'], result['ptag'])</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(pandas.crosstab(result['tag'], result['ptag']))</span></span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"> </span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> result.to_csv(args.output)</span>
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/bin/evs_exportmodel.py</span></span>
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/bin/evs_exportmodel.py</span></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" 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="LC637" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/bin/evs_learn.py</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/bin/evs_learn.py</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC644" 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="LC645" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span> def parseArgs():</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"> help="Which model to use (options are: %s)" % str(modelNames))</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"> </span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> parser.add_argument("--features",</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- choices=evs.features.FeatureSet.sets.keys(),</span></span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ choices=list(evs.features.FeatureSet.sets.keys()),</span></span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"> required=True,</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"> help="Training features. Either a feature-table name or a comma-separated list of feature names."</span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"> " e.g. QSS_NT,T_DP_RATE")</span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="p">@@ -109,7 +109,7 @@</span> def getDataSet(inputs, args) :</span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"> datasets = []</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"> for inputFile in inputs:</span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"> inputFile = os.path.abspath(inputFile)</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading '%s'" % (inputFile)</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading '%s'" % (inputFile))</span></span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"> df = pandas.read_csv(inputFile, na_values=".")</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> df.fillna("0", inplace=True)</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> # Remove false negatives before any subsampling:</span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"><span class="p">@@ -125,9 +125,9 @@</span> def getDataSet(inputs, args) :</span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"> fps = df[df["tag"] == "FP"]</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"> if args.ambig:</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> ambigs = df[df["tag"] == "UNK"]</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "TP: %d FP: %d, UNK: %d" % (tps.shape[0], fps.shape[0], ambigs.shape[0])</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("TP: %d FP: %d, UNK: %d" % (tps.shape[0], fps.shape[0], ambigs.shape[0]))</span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"> else:</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "TP: %d FP: %d" % (tps.shape[0], fps.shape[0])</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("TP: %d FP: %d" % (tps.shape[0], fps.shape[0]))</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> if tps.shape[0] < fps.shape[0]:</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> rows_selected = random.sample(fps.index, tps.shape[0])</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"> fps = pandas.DataFrame(fps.ix[rows_selected])</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="p">@@ -142,10 +142,10 @@</span> def getDataSet(inputs, args) :</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> if args.ambig:</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> rows_selected = random.sample(ambigs.index, fps.shape[0])</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> ambigs = pandas.DataFrame(ambigs.ix[rows_selected])</span>
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<td class="diff-line-num new new_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Downsampled to TP: %d, FP: %d, UNK: %d" % (tps.shape[0], fps.shape[0], ambigs.shape[0])</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Downsampled to TP: %d, FP: %d, UNK: %d" % (tps.shape[0], fps.shape[0], ambigs.shape[0]))</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> df = pandas.concat([tps, fps, ambigs])</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> else:</span>
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<td class="diff-line-num new new_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Downsampled to TP: %d FP: %d" % (tps.shape[0], fps.shape[0])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Downsampled to TP: %d FP: %d" % (tps.shape[0], fps.shape[0]))</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> df = pandas.concat([tps, fps])</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> </span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> df["weight"] = 1</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="p">@@ -171,9 +171,9 @@</span> def main():</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> pars = {}</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"> if args.parameters :</span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> pars = json.load(open(args.parameters))</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Using custom learning parameters: %s" % str(pars)</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Using custom learning parameters: %s" % str(pars))</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> else :</span>
</pre>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Using default learning parameters."</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Using default learning parameters.")</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"> </span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"> model = evs.EVSModel.createNew(args.model)</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> </span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="p">@@ -210,7 +210,7 @@</span> def main():</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"> if args.plots and hasattr(model, "plots"):</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"> model.plots(args.output + ".plots", features)</span>
</pre>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"> elif args.plots:</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "No plots created, this is not supported by %s" % args.model</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("No plots created, this is not supported by %s" % args.model)</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"> </span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"> </span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"> if __name__ == '__main__':</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/bin/evs_pr.py</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/bin/evs_pr.py</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> #</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="p">@@ -71,7 +71,7 @@</span> def main():</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"> datasets = []</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> for i in args.inputs:</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"> i = os.path.abspath(i)</span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> df = pandas.read_csv(i)</span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> datasets.append(df)</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"> </span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="p">@@ -190,7 +190,7 @@</span> def main():</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"> </span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> counter += 1</span>
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<td class="diff-line-num new new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"> if counter % 10 == 0:</span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Processed %i / %i qual values for %s" % (counter, len(qual_vals), f)</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Processed %i / %i qual values for %s" % (counter, len(qual_vals), f))</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"> </span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"> cols=["field", "qual", "tp", "fp", "fn","tp_filtered", "fp_filtered", "na", "na_filtered", "precision", "recall", "fracNA"]</span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"> if args.stratify :</span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/bin/evs_qq.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/bin/evs_qq.py</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"> #</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="p">@@ -72,7 +72,7 @@</span> def main():</span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> datasets = []</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"> for i in args.inputs:</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"> i = os.path.abspath(i)</span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"> df = pandas.read_csv(i)</span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"> datasets.append(df)</span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"> </span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="p">@@ -87,12 +87,12 @@</span> def main():</span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> result = []</span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"> regression = []</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"> </span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Total: %d" % len(dataset)</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Total: %d" % len(dataset))</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"> fns = dataset[dataset["tag"] == "FN"].shape[0]</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "fn: %d" % fns</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "tp: %d" % len(dataset[dataset["tag"] == "TP"])</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "fp: %d" % len(dataset[dataset["tag"] == "FP"])</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "unk: %d" % len(dataset[dataset["tag"] == "UNK"])</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("fn: %d" % fns)</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("tp: %d" % len(dataset[dataset["tag"] == "TP"]))</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("fp: %d" % len(dataset[dataset["tag"] == "FP"]))</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("unk: %d" % len(dataset[dataset["tag"] == "UNK"]))</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"> dataset = pandas.DataFrame(dataset[dataset["tag"].isin(["TP", "FP"])])</span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"> data = pandas.DataFrame(dataset.dropna(subset=["qual"]))</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"> data = data.iloc[numpy.random.permutation(len(data))] # shuffle before sorting: this ensures random order within tied groups</span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="p">@@ -120,7 +120,7 @@</span> def main():</span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"> </span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"> counter += 1</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"> if counter % 10 == 0:</span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Processed %i / %i values" % (counter, len(bins))</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Processed %i / %i values" % (counter, len(bins)))</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"> </span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"> df = pandas.DataFrame(result)</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"> df["Q"] = phred(df["qual"])</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"><span class="p">@@ -128,8 +128,8 @@</span> def main():</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"> regr = linear_model.LinearRegression()</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"> regr.fit(phred(df["qual"]).reshape(-1,1), phred(df["precision"]).reshape(-1,1))</span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"> df["calibratedQ"] = regr.predict(phred(df["qual"]).reshape(-1,1))</span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print df</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Coefficient: {}, Intercept: {}".format(regr.coef_[0,0], regr.intercept_[0]))</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(df)</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("Coefficient: {}, Intercept: {}".format(regr.coef_[0,0], regr.intercept_[0])))</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"> df.to_csv(args.output)</span>
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"> json.dump({"Coefficient" : regr.coef_[0,0], "Intercept" : regr.intercept_[0]}, open(args.calibration, 'w'))</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/bin/filterTrainingVcf.py</span></span>
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/bin/filterTrainingVcf.py</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"> #</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/bin/parseAnnotatedTrainingVcf.py</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/bin/parseAnnotatedTrainingVcf.py</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<pre style="margin: 0;">+<span id="LC805" 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="LC806" class="line" lang="diff"> #</span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/__init__.py</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"><span class="p">@@ -25,11 +25,9 @@</span> import evs.tools.io as io</span>
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class EVSModel(object):</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class EVSModel(object, metaclass=abc.ABCMeta):</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"> """ Base class for EVS models """</span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __metaclass__ = abc.ABCMeta</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"> def __init__(self):</span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> self.clf = None</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"> self.mname = None</span>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="p">@@ -95,8 +93,8 @@</span> class EVSModel(object):</span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"> </span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"> @classmethod</span>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"> def names(cls):</span>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return cls._models.keys()</span></span>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return list(cls._models.keys())</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> </span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"> </span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import germline_rf # noqa</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import germline_rf # noqa</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"> </span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/features/GermlineIndel.py</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/features/GermlineIndel.py</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"> #</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"> #</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"> </span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from VcfFeatureSet import VcfFeatureSet</span></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .VcfFeatureSet import VcfFeatureSet</span></span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"> </span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"> </span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"> @VcfFeatureSet.register("germline.indel")</span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/features/GermlineSNV.py</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/features/GermlineSNV.py</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"> #</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="diff"> #</span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="diff"> </span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from VcfFeatureSet import VcfFeatureSet</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .VcfFeatureSet import VcfFeatureSet</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"> </span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"> </span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"> @VcfFeatureSet.register("germline.snv")</span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/features/RNAIndel.py</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/features/RNAIndel.py</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="diff"> #</span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="diff"> #</span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="diff"> </span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from VcfFeatureSet import VcfFeatureSet</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .VcfFeatureSet import VcfFeatureSet</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="diff"> </span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="diff"> </span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="diff"> @VcfFeatureSet.register("rna.indel")</span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/features/RNASNV.py</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/features/RNASNV.py</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="diff"> #</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from VcfFeatureSet import VcfFeatureSet</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .VcfFeatureSet import VcfFeatureSet</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"> </span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"> </span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"> @VcfFeatureSet.register("rna.snv")</span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/features/__init__.py</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/features/__init__.py</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="diff"><span class="p">@@ -20,11 +20,9 @@</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="diff"> import abc</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="diff"> </span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="diff"> </span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class FeatureSet(object):</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class FeatureSet(object, metaclass=abc.ABCMeta):</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="diff"> """ VCF paired Feature set for somatic comparison """</span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="diff"> </span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __metaclass__ = abc.ABCMeta</span></span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="diff"> def __init__(self):</span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="diff"> pass</span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="diff"> </span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="diff"><span class="p">@@ -56,7 +54,7 @@</span> class FeatureSet(object):</span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="diff"> return FeatureSet.sets[name]()</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="diff"> </span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="diff"> </span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import GermlineSNV # noqa</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import GermlineIndel # noqa</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import RNASNV # noqa</span></span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import RNAIndel # noqa</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import GermlineSNV # noqa</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import GermlineIndel # noqa</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import RNASNV # noqa</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import RNAIndel # noqa</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/germline_rf.py</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/germline_rf.py</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="diff"><span class="p">@@ -114,13 +114,13 @@</span> class GermlineRF(EVSModel):</span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="diff"> indices = np.argsort(importances)[::-1]</span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="diff"> </span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="diff"> # Print the feature ranking</span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Feature ranking:"</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Feature ranking:")</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="diff"> </span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for f in xrange(0, len(indices)):</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%d. feature %d:%s (%f +- %f)" % (f + 1, indices[f],</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for f in range(0, len(indices)):</span></span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%d. feature %d:%s (%f +- %f)" % (f + 1, indices[f],</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="diff"> featurenames[indices[f]],</span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="diff"> importances[indices[f]],</span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std[indices[f]])</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std[indices[f]]))</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="diff"> </span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="diff"> def draw_trees(self):</span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="diff"> """ Draw trees in png files """</span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/germline/lib/evs/tools/io.py</span></span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/germline/lib/evs/tools/io.py</span></span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="diff"> </span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="diff"> import os</span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="diff"> import sys</span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle</span></span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle</span></span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="diff"> import json</span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="diff"> </span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="diff"> </span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="diff"><span class="p">@@ -58,14 +58,14 @@</span> def dict_for_tree(tree):</span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="diff"> def read_pickled_classifier(pickle_fn):</span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="diff"> """ Read classifier from pickle file """</span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="diff"> with open(pickle_fn, 'rb') as fid:</span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- clf = cPickle.load(fid)</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ clf = pickle.load(fid)</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="diff"> return clf</span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="diff"> </span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="diff"> </span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="diff"> def write_classifier_pickle(clf, pickle_fn):</span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="diff"> """ store classifier in pickle file """</span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="diff"> with open(pickle_fn, 'wb') as fid:</span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cPickle.dump(clf, fid)</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pickle.dump(clf, fid)</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="diff"> </span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="diff"> def classifier_to_dict(clf):</span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/calc_features.py</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/calc_features.py</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="diff"> #</span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="diff"><span class="p">@@ -69,7 +69,7 @@</span> def main():</span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="diff"> datasets = []</span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="diff"> for i in args.inputs:</span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="diff"> i = os.path.abspath(i)</span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="diff"> df = pandas.read_csv(i)</span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="diff"> datasets.append(df)</span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="diff"> </span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/evs_evaluate.py</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/evs_evaluate.py</span></span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="diff"> #</span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<td class="diff-line-num new new_line" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="diff"><span class="p">@@ -50,7 +50,7 @@</span> def parseArgs():</span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="diff"> parser.add_argument("-c", "--classifier", required=True,</span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="diff"> help="Classifier pickle file name")</span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="diff"> parser.add_argument("-f", "--features",</span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- choices=evs.features.FeatureSet.sets.keys(),</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ choices=list(evs.features.FeatureSet.sets.keys()),</span></span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="diff"> required=True,</span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="diff"> help="Which feature set to use (or a comma-separated list of feature names,"</span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="diff"> " e.g. -f QSS_NT,T_DP_RATE")</span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span> def main():</span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="diff"> datasets = []</span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="diff"> for i in args.inputs:</span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="diff"> i = os.path.abspath(i)</span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="diff"> df = pandas.read_csv(i)</span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="diff"> datasets.append(df)</span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="diff"> </span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="diff"><span class="p">@@ -114,7 +114,7 @@</span> def main():</span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="diff"> </span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="diff"> result = pandas.concat(rlist)</span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="diff"> </span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print pandas.crosstab(result['tag'], result['ptag'])</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(pandas.crosstab(result['tag'], result['ptag']))</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="diff"> </span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="diff"> result.to_csv(args.output)</span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="diff"> </span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/evs_exportmodel.py</span></span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/evs_exportmodel.py</span></span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="diff"> #</span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/evs_learn.py</span></span>
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1015
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<pre style="margin: 0;">+<span id="LC1015" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/evs_learn.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1016
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<pre style="margin: 0;">+<span id="LC1016" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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1017
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<pre style="margin: 0;">+<span id="LC1017" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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1018
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<pre style="margin: 0;">+<span id="LC1018" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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1019
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<pre style="margin: 0;">+<span id="LC1019" class="line" lang="diff"> #</span>
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1020
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<pre style="margin: 0;">+<span id="LC1020" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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1021
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<pre style="margin: 0;">+<span id="LC1021" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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1022
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<pre style="margin: 0;">+<span id="LC1022" class="line" lang="diff"><span class="p">@@ -56,7 +56,7 @@</span> def parseArgs():</span>
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<td class="diff-line-num new new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1023
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<pre style="margin: 0;">+<span id="LC1023" class="line" lang="diff"> help="Which model to use (options are: %s)" % str(modelNames))</span>
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1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="diff"> </span>
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1025
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<pre style="margin: 0;">+<span id="LC1025" class="line" lang="diff"> parser.add_argument("--features",</span>
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1026
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<pre style="margin: 0;">+<span id="LC1026" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- choices=evs.features.FeatureSet.sets.keys(),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ choices=list(evs.features.FeatureSet.sets.keys()),</span></span>
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1028
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<pre style="margin: 0;">+<span id="LC1028" class="line" lang="diff"> required=True,</span>
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1029
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<pre style="margin: 0;">+<span id="LC1029" class="line" lang="diff"> help="Training features. Either a feature-table name or a comma-separated list of feature names."</span>
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<td class="diff-line-num new new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1030
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<pre style="margin: 0;">+<span id="LC1030" class="line" lang="diff"> " e.g. QSS_NT,T_DP_RATE")</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="diff"><span class="p">@@ -110,7 +110,7 @@</span> def getDataSet(inputs, sample_input, bal</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="diff"> for inputFile in inputs:</span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="diff"> inputFile = os.path.abspath(inputFile)</span>
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<td class="diff-line-num new new_line" data-linenumber="1035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1035
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<pre style="margin: 0;">+<span id="LC1035" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading '%s'" % (inputFile)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1036
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<pre style="margin: 0;">+<span id="LC1036" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading '%s'" % (inputFile))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1037
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<pre style="margin: 0;">+<span id="LC1037" class="line" lang="diff"> df = pandas.read_csv(inputFile)</span>
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<td class="diff-line-num new new_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1038
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<pre style="margin: 0;">+<span id="LC1038" class="line" lang="diff"> # Remove false negatives before any subsampling:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1039
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<pre style="margin: 0;">+<span id="LC1039" class="line" lang="diff"> df = df[df["tag"] != "FN"]</span>
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<td class="diff-line-num new new_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1040
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<pre style="margin: 0;">+<span id="LC1040" class="line" lang="diff"><span class="p">@@ -123,23 +123,23 @@</span> def getDataSet(inputs, sample_input, bal</span>
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<td class="diff-line-num new new_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1041
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<pre style="margin: 0;">+<span id="LC1041" class="line" lang="diff"> if balance_per_sample:</span>
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<td class="diff-line-num new new_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="diff"> tps = df[df["tag"] == "TP"]</span>
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<td class="diff-line-num new new_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="diff"> fps = df[df["tag"] == "FP"]</span>
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<td class="diff-line-num new new_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1044
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<pre style="margin: 0;">+<span id="LC1044" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "TP: %d FP: %d" % (tps.shape[0], fps.shape[0])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("TP: %d FP: %d" % (tps.shape[0], fps.shape[0]))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="diff"> if tps.shape[0] < fps.shape[0]:</span>
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<td class="diff-line-num new new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1047
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<pre style="margin: 0;">+<span id="LC1047" class="line" lang="diff"> rows_selected = random.sample(fps.index, tps.shape[0])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="diff"> fps = pandas.DataFrame(fps.ix[rows_selected])</span>
</pre>
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1049
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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="diff"> elif fps.shape[0] < tps.shape[0]:</span>
</pre>
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1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="diff"> rows_selected = random.sample(tps.index, fps.shape[0])</span>
</pre>
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1051
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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="diff"> tps = pandas.DataFrame(tps.ix[rows_selected])</span>
</pre>
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1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Downsampled to TP: %d FP: %d" % (tps.shape[0], fps.shape[0])</span></span>
</pre>
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1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Downsampled to TP: %d FP: %d" % (tps.shape[0], fps.shape[0]))</span></span>
</pre>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="diff"> df = pandas.concat([tps, fps])</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="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1055
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1055" class="line" lang="diff"> </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="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1056
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1056" class="line" lang="diff"> df["weight"] = 1</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="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1057
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1057" class="line" lang="diff"> if "Admix" in inputFile:</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="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1058
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1058" class="line" lang="diff"> df["weight"] = admixWeight</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="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1059
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1059" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Admixture: setting weight to %f" % admixWeight</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="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1060
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1060" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Admixture: setting weight to %f" % admixWeight)</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="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1061
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1061" class="line" lang="diff"> if "NN" in inputFile:</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="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1062
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1062" class="line" lang="diff"> df["weight"] = nnWeight</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="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1063
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1063" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Normal-normal: setting weight to %f" % nnWeight</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="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1064
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1064" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Normal-normal: setting weight to %f" % nnWeight)</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="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1065
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1065" class="line" lang="diff"> datasets.append(df)</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="1066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1066
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1066" class="line" lang="diff"> </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="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1067
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1067" class="line" lang="diff"> if len(datasets) > 1:</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="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1068
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1068" class="line" lang="diff"><span class="p">@@ -163,9 +163,9 @@</span> def main():</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="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1069
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1069" class="line" lang="diff"> pars = {}</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="1070" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1070
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1070" class="line" lang="diff"> if args.parameters :</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="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1071
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1071" class="line" lang="diff"> pars = json.load(open(args.parameters))</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="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1072
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1072" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Using custom learning parameters: %s" % str(pars)</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="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1073
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1073" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Using custom learning parameters: %s" % str(pars))</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="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1074" class="line" lang="diff"> else :</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="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1075
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1075" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Using default learning parameters."</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="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1076
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1076" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Using default learning parameters.")</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="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1077" class="line" lang="diff"> </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="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1078
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1078" class="line" lang="diff"> model = evs.EVSModel.createNew(args.model)</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="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1079
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1079" class="line" lang="diff"> </span>
</pre>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="diff"><span class="p">@@ -189,7 +189,7 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="diff"> if args.plots and hasattr(model, "plots"):</span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="diff"> model.plots(args.output + ".plots", features)</span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="diff"> elif args.plots:</span>
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<td class="diff-line-num new new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "No plots created, this is not supported by %s" % args.model</span></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("No plots created, this is not supported by %s" % args.model)</span></span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="diff"> </span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="diff"> </span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="diff"> if __name__ == '__main__':</span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/evs_pr.py</span></span>
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1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/evs_pr.py</span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="diff"> #</span>
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1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="diff"><span class="p">@@ -69,7 +69,7 @@</span> def main():</span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="diff"> datasets = []</span>
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1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="diff"> for i in args.inputs:</span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="diff"> i = os.path.abspath(i)</span>
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1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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1102
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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="diff"> df = pandas.read_csv(i)</span>
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1104
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<pre style="margin: 0;">+<span id="LC1104" class="line" lang="diff"> datasets.append(df)</span>
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1105
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<pre style="margin: 0;">+<span id="LC1105" class="line" lang="diff"> </span>
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1106
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<pre style="margin: 0;">+<span id="LC1106" class="line" lang="diff"><span class="p">@@ -121,12 +121,12 @@</span> def main():</span>
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1107
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<pre style="margin: 0;">+<span id="LC1107" class="line" lang="diff"> strelka_f_fps = strelka_def_f[</span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="diff"> strelka_def_f["tag"] == "FP"].shape[0]</span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Strelka default filtering:"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "NT != ref: %i" % dataset[True != strelka_f_ref].shape[0]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "iHpol: %i" % dataset[True != strelka_f_ihpol].shape[0]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "BCNoise: %i" % dataset[True != strelka_f_bcnoise].shape[0]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Repeat: %i" % dataset[True != strelka_f_repeat].shape[0]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Total: %i (%i TP and %i FP)" % (dataset[True != strelka_f].shape[0], strelka_f_tps, strelka_f_fps)</span></span>
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1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Strelka default filtering:")</span></span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("NT != ref: %i" % dataset[True != strelka_f_ref].shape[0])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("iHpol: %i" % dataset[True != strelka_f_ihpol].shape[0])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("BCNoise: %i" % dataset[True != strelka_f_bcnoise].shape[0])</span></span>
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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Repeat: %i" % dataset[True != strelka_f_repeat].shape[0])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Total: %i (%i TP and %i FP)" % (dataset[True != strelka_f].shape[0], strelka_f_tps, strelka_f_fps))</span></span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="diff"> </span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="diff"> data_remaining = dataset[True == strelka_f]</span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="diff"> else:</span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="diff"><span class="p">@@ -158,7 +158,7 @@</span> def main():</span>
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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="diff"> </span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="diff"> counter += 1</span>
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1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="diff"> if counter % 10 == 0:</span>
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<td class="diff-line-num new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Processed %i / %i qual values for %s" % (counter, len(qual_vals), f)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Processed %i / %i qual values for %s" % (counter, len(qual_vals), f))</span></span>
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1131
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="diff"> </span>
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1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="diff"> pandas.DataFrame(result, columns=[</span>
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<td class="diff-line-num new new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="diff"> "field", "qual", "tp", "fp", "fn",</span>
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<td class="diff-line-num new new_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/evs_random_sample_tpfp.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/evs_random_sample_tpfp.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="diff"> #</span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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<td class="diff-line-num new new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<td class="diff-line-num new new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="diff"><span class="p">@@ -55,7 +55,7 @@</span> def main():</span>
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<td class="diff-line-num new new_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="diff"> datasets = []</span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="diff"> for i in args.inputs:</span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="diff"> i = os.path.abspath(i)</span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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1147
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<pre style="margin: 0;">+<span id="LC1147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="diff"> df = pandas.read_csv(i)</span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="diff"> datasets.append(df)</span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="diff"> </span>
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1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="diff"><span class="p">@@ -70,7 +70,7 @@</span> def main():</span>
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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="diff"> nrows = min([tpdata2.shape[0], fpdata2.shape[0]])</span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="diff"> </span>
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1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="diff"> if nrows < args.samplesize:</span>
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1155
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<pre style="margin: 0;">+<span id="LC1155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print >> sys.stderr, "Warning: sampling will use some records multiple times because there is not enough data!"</span></span>
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1156
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<pre style="margin: 0;">+<span id="LC1156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Warning: sampling will use some records multiple times because there is not enough data!", file=sys.stderr)</span></span>
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1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="diff"> </span>
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1158
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<pre style="margin: 0;">+<span id="LC1158" class="line" lang="diff"> tp_rows_selected = random.sample(tpdata2.index, args.samplesize)</span>
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1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="diff"> fp_rows_selected = random.sample(fpdata2.index, args.samplesize)</span>
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1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/evs_random_split_csv.py</span></span>
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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/evs_random_split_csv.py</span></span>
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1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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1163
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<pre style="margin: 0;">+<span id="LC1163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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1164
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<pre style="margin: 0;">+<span id="LC1164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="diff"> #</span>
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1166
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<pre style="margin: 0;">+<span id="LC1166" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="diff"><span class="p">@@ -57,7 +57,7 @@</span> def main():</span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="diff"> datasets = []</span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="diff"> for i in args.inputs:</span>
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1171
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<pre style="margin: 0;">+<span id="LC1171" class="line" lang="diff"> i = os.path.abspath(i)</span>
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1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Reading %s" % i</span></span>
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1173
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<pre style="margin: 0;">+<span id="LC1173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Reading %s" % i)</span></span>
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1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="diff"> df = pandas.read_csv(i)</span>
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1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="diff"> datasets.append(df)</span>
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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="diff"> </span>
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1177
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<pre style="margin: 0;">+<span id="LC1177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/bin/vcf_to_feature_csv.py</span></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/bin/vcf_to_feature_csv.py</span></span>
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1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="diff"> #</span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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1184
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<pre style="margin: 0;">+<span id="LC1184" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span>
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span> def parseArgs():</span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="diff"> help="Bed file conforming to the curium ambiguous region file format"</span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="diff"> " (may be specified more than once)")</span>
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1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="diff"> parser.add_argument("--features", required=True,</span>
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1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- choices=evs.features.FeatureSet.sets.keys(),</span></span>
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1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ choices=list(evs.features.FeatureSet.sets.keys()),</span></span>
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="diff"> help="Select a feature table to output.")</span>
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1193" class="line" lang="diff"> args = parser.parse_args()</span>
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC1196" class="line" lang="diff"><span class="p">@@ -25,11 +25,9 @@</span> import evs.tools.io as io</span>
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<pre style="margin: 0;">+<span id="LC1197" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1199" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class EVSModel(object):</span></span>
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class EVSModel(object, metaclass=abc.ABCMeta):</span></span>
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="diff"> """ Base class for EVS models """</span>
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __metaclass__ = abc.ABCMeta</span></span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1206
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<pre style="margin: 0;">+<span id="LC1206" class="line" lang="diff"> def __init__(self):</span>
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="diff"> self.clf = None</span>
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1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="diff"> self.mname = None</span>
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="diff"><span class="p">@@ -95,7 +93,7 @@</span> class EVSModel(object):</span>
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1211" class="line" lang="diff"> @classmethod</span>
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="diff"> def names(cls):</span>
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return cls._models.keys()</span></span>
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return list(cls._models.keys())</span></span>
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import somatic_rf # noqa</span></span>
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import somatic_rf # noqa</span></span>
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/features/PosAndAlleles.py</span></span>
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<pre style="margin: 0;">+<span id="LC1220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/features/PosAndAlleles.py</span></span>
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from VcfFeatureSet import VcfFeatureSet</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1226" style="width: 35px; color: rgba(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="LC1226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .VcfFeatureSet import VcfFeatureSet</span></span>
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="diff"> @VcfFeatureSet.register("posandalleles")</span>
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1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/features/SomaticIndel.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/features/SomaticIndel.py</span></span>
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1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="diff"> #</span>
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1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="diff"> #</span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from VcfFeatureSet import VcfFeatureSet</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .VcfFeatureSet import VcfFeatureSet</span></span>
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1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="diff"> </span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="diff"> </span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="diff"> @VcfFeatureSet.register("somatic.indel")</span>
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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/features/SomaticSNV.py</span></span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/features/SomaticSNV.py</span></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>
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1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="diff"> #</span>
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1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="diff"> #</span>
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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from VcfFeatureSet import VcfFeatureSet</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from .VcfFeatureSet import VcfFeatureSet</span></span>
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1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="diff"> </span>
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1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="diff"> </span>
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1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="diff"> @VcfFeatureSet.register("somatic.snv")</span>
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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/features/__init__.py</span></span>
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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/features/__init__.py</span></span>
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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="diff"><span class="p">@@ -20,11 +20,9 @@</span></span>
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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="diff"> import abc</span>
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1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="diff"> </span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="diff"> </span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-class FeatureSet(object):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+class FeatureSet(object, metaclass=abc.ABCMeta):</span></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="diff"> """ VCF paired Feature set for somatic comparison """</span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="diff"> </span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- __metaclass__ = abc.ABCMeta</span></span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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1264
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="diff"> def __init__(self):</span>
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1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="diff"> pass</span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="diff"><span class="p">@@ -56,6 +54,6 @@</span> class FeatureSet(object):</span>
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="diff"> return FeatureSet.sets[name]()</span>
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1269
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="diff"> </span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="diff"> </span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import SomaticSNV # noqa</span></span>
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1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import SomaticIndel # noqa</span></span>
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1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import PosAndAlleles # noqa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import SomaticSNV # noqa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import SomaticIndel # noqa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import PosAndAlleles # noqa</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/somatic_rf.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/somatic_rf.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="diff"><span class="p">@@ -108,12 +108,12 @@</span> class SomaticRF(EVSModel):</span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="diff"> indices = np.argsort(importances)[::-1]</span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="diff"> </span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="diff"> # Print the feature ranking</span>
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<td class="diff-line-num new new_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Feature ranking:"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Feature ranking:")</span></span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for f in xrange(0, len(indices)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%d. feature %d:%s (%f +- %f)" % (f + 1, indices[f],</span></span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for f in range(0, len(indices)):</span></span>
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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%d. feature %d:%s (%f +- %f)" % (f + 1, indices[f],</span></span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="diff"> featurenames[indices[f]],</span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="diff"> importances[indices[f]],</span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std[indices[f]])</span></span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std[indices[f]]))</span></span>
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1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="diff"> </span>
</pre>
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1295
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<pre style="margin: 0;">+<span id="LC1295" class="line" lang="diff"> EVSModel.register("somatic.rf", SomaticRF)</span>
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1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/strelka_rf_indel.py</span></span>
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1297
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<pre style="margin: 0;">+<span id="LC1297" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/strelka_rf_indel.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="diff"><span class="p">@@ -112,12 +112,12 @@</span> class StrelkaRFIndel(EVSModel):</span>
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1299
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<pre style="margin: 0;">+<span id="LC1299" class="line" lang="diff"> indices = np.argsort(importances)[::-1]</span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="diff"> </span>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="diff"> # Print the feature ranking</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Feature ranking for INDELTYPE == %s:" % str(it)</span></span>
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1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("Feature ranking for INDELTYPE == %s:" % str(it))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for f in xrange(0, len(indices)):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "%d. feature %d:%s (%f +- %f)" % (f + 1, indices[f],</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for f in range(0, len(indices)):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("%d. feature %d:%s (%f +- %f)" % (f + 1, indices[f],</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="diff"> featurenames[indices[f]],</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="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="diff"> importances[indices[f]],</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="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1311
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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="LC1311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- std[indices[f]])</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="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1312
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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="LC1312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ std[indices[f]]))</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="diff"> </span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="diff"> EVSModel.register("strelka.rf.indel", StrelkaRFIndel)</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="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/python/scoringModelTraining/somatic/lib/evs/tools/io.py</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="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/python/scoringModelTraining/somatic/lib/evs/tools/io.py</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="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1317
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<pre style="margin: 0;">+<span id="LC1317" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</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="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1318
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<pre style="margin: 0;">+<span id="LC1318" 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="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="diff"> import os</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="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="diff"> import sys</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="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import cPickle</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="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import pickle</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="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="diff"> import json</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="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1324
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<pre style="margin: 0;">+<span id="LC1324" 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="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="diff"> </span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="diff"><span class="p">@@ -58,14 +58,14 @@</span> def dict_for_tree(tree):</span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="diff"> def read_pickled_classifier(pickle_fn):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="diff"> """ Read classifier from pickle file """</span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="diff"> with open(pickle_fn, 'rb') as fid:</span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- clf = cPickle.load(fid)</span></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ clf = pickle.load(fid)</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="diff"> return clf</span>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="diff"> </span>
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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="diff"> def write_classifier_pickle(clf, pickle_fn):</span>
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1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="diff"> """ store classifier in pickle file """</span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="diff"> with open(pickle_fn, 'wb') as fid:</span>
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1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cPickle.dump(clf, fid)</span></span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pickle.dump(clf, fid)</span></span>
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1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="diff"> </span>
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1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="diff"> </span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="diff"> def classifier_to_dict(clf):</span>
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1343
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<pre style="margin: 0;">+<span id="LC1343" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/srcqc/run_cppcheck.py</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/srcqc/run_cppcheck.py</span></span>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" 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="LC1348" class="line" lang="diff"> #</span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="diff"> # Strelka - Small Variant Caller</span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="diff"> # Copyright (c) 2009-2018 Illumina, Inc.</span></pre>
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<a href="https://salsa.debian.org/med-team/strelka/-/compare/8f85277cf3b3cb42417a2bd3fad7748f39f45b63...7fbdd9e5cf6633fe93e43b3e7e8e753a3a5a30f3#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2to3.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/strelka/-/compare/8f85277cf3b3cb42417a2bd3fad7748f39f45b63...7fbdd9e5cf6633fe93e43b3e7e8e753a3a5a30f3#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -17,16 +17,11 @@ include /usr/share/dpkg/default.mk</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</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">CMAKE_EXTRA_FLAGS += \</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> FULL_PREFIX=/usr \</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> THIS_DATADIR=share/$(DEB_SOURCE) \</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> THIS_MODULE_DIR=cmake</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> dh $@ --<span class="idiff left right">sourcedirectory=src</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh $@ --<span class="idiff left right">buildsystem=cmake</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> dh_auto_configure -- <span class="idiff left right">$(CMAKE_EXTRA_FLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> dh_auto_configure -- <span class="idiff left right">-DCMAKE_BUILD_TYPE=RelWithDebInfo</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">#override_dh_auto_test:</span>
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