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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libsonlib">Debian Med / libsonlib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsonlib/-/commit/afd7c23cf3785a2263175135ec666c83a2cdd211">afd7c23c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T10:41:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build against libquicktree-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libsonlib/-/commit/d9c8af3536608e3f936d0b605040aaca2861b4be">d9c8af35</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T11:36:03+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try really hard to get tests run
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/libsonlib/-/commit/e02ce9f8e568331b7320aaad5855e7fa59c8b051">e02ce9f8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-16T11:43:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Build-Depends: tokyocabinet
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#f168b81935360ddcf2dd0f2d4b98b8603829060f">
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debian/README.Debian
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<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
<span class="new-file">
+
debian/clean
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
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+
debian/patches/2to3.patch
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<a href="#82e0bda1ef781bbe11386f41bc18524910c179a4">
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debian/patches/fix_test.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#51664dd3d87bd8d260785cd9b786f636afb4c7dd">
debian/patches/use_debian_packaged_quicktree.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sonLib for Debian</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=================</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">SonLib is originally shipped with a code copy of quicktree. To avoid</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">duplicated code the Debian package also builds a static library. If you</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">want to use sonLib in your code you need to add</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> CFLAGS += -I/usr/include/quicktree</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> LIBS += -lquicktree</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">to build successfully.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 16 Jun 2020 08:23:45 +0200</span></pre>
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<li id="f5f51601866c86e59a004bd93fa415f5675be8c5">
<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sonLib_daemonize.py</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python3<span class="idiff left right">-all-dev</span>,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> python3,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> libquicktree-dev,</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> zlib1g-dev,</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libtokyocabinet-dev,</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libbz2-dev</span>
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10
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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11
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/libsonlib</span>
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12
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/libsonlib.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,7 +21,7 @@ Section: libdevel</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right">quicktree</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right">libquicktree-dev</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Description: compact C/Python library for sequence analysis in bioinformatics</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> SonLib is a small general purpose library for C and Python for sequence</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> analysis with focus on bioinformatics.</span>
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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">
<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#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="gd" style="color: #000; background-color: #fdd;">--- a/C/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/C/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -65,4 +65,4 @@</span> ${libPath}/sonLib.a : ${libSources} ${cp</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> mv sonLib.a ${libPath}/</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> test:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python allTests.py --testLength=SHORT --logLevel CRITICAL</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ python3 allTests.py --testLength=SHORT --logLevel CRITICAL</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span> externalToolsP.clean :</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> cd externalTools && make clean</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> test : all</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PYTHONPATH=.. PATH=../../bin:$$PATH python allTests.py --testLength=SHORT --logLevel=CRITICAL</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PYTHONPATH=.. PATH=../../bin:$$PATH python3 allTests.py --testLength=SHORT --logLevel=CRITICAL</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> ${binPath}/sonLib_daemonize.py : sonLib_daemonize.py</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> cp sonLib_daemonize.py ${binPath}/sonLib_daemonize.py</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</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;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> from setuptools import setup, find_packages</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> #import subprocess</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/src/sonLib/__init__.py</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/src/sonLib/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/bioio.py</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/bioio.py</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></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;">-#!/usr/bin/env python</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;">+#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -421,14 +421,14 @@</span> def nameValue(name, value, valueType=str</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> def getRandomAlphaNumericString(length=10):</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> """Returns a random alpha numeric string of the given length.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return "".join([ random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz') for i in xrange(0, length) ])</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return "".join([ random.choice('0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz') for i in range(0, length) ])</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> def makeSubDir(dirName):</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> """Makes a given subdirectory if it doesn't already exist, making sure it us public.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> if not os.path.exists(dirName):</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> os.mkdir(dirName)</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.chmod(dirName, 0777)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.chmod(dirName, 0o777)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> return dirName</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> def getTempFile(suffix="", rootDir=None):</span>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="p">@@ -441,7 +441,7 @@</span> def getTempFile(suffix="", rootDir=None)</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> else:</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> tmpFile = os.path.join(rootDir, "tmp_" + getRandomAlphaNumericString() + suffix)</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> open(tmpFile, 'w').close()</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.chmod(tmpFile, 0777) #Ensure everyone has access to the file.</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.chmod(tmpFile, 0o777) #Ensure everyone has access to the file.</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> return tmpFile</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> def getTempDirectory(rootDir=None):</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -468,7 +468,7 @@</span> def getTempDirectory(rootDir=None):</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> break</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> os.mkdir(tmpDir)</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- os.chmod(tmpDir, 0777) #Ensure everyone has access to the file.</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ os.chmod(tmpDir, 0o777) #Ensure everyone has access to the file.</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> return tmpDir</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> </span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> class TempFileTree:</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -744,7 +744,7 @@</span> def fastaWrite(fileHandleOrFile, name, s</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> fileHandle = _getFileHandle(fileHandleOrFile, mode)</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> valid_chars = {x for x in string.ascii_letters + "-"}</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> try:</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert any([isinstance(seq, unicode), isinstance(seq, str)])</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert any([isinstance(seq, str), isinstance(seq, str)])</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> except AssertionError:</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> raise RuntimeError("Sequence is not unicode or string")</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> try:</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -754,7 +754,7 @@</span> def fastaWrite(fileHandleOrFile, name, s</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> raise RuntimeError("Invalid FASTA character(s) see in fasta sequence: {}".format(bad_chars))</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> fileHandle.write(">%s\n" % name)</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> chunkSize = 100</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, len(seq), chunkSize):</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, len(seq), chunkSize):</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> fileHandle.write("%s\n" % seq[i:i+chunkSize])</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> if isinstance(fileHandleOrFile, "".__class__):</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> fileHandle.close()</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -849,23 +849,23 @@</span> def fastaAlignmentRead(fasta, mapFn=(lam</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> else:</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> l = l[:]</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> seqNo = len(l)</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, seqNo):</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, seqNo):</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> j = open(fasta, 'r')</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> j.seek(l[i])</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> l[i] = j</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- column = [sys.maxint]*seqNo</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ column = [sys.maxsize]*seqNo</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> if seqNo != 0:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> while True:</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(0, seqNo):</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(0, seqNo):</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> i = l[j].read(1)</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> while i == '\n':</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> i = l[j].read(1)</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> column[j] = i</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> if column[0] == '>' or column[0] == '':</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(1, seqNo):</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(1, seqNo):</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> assert column[j] == '>' or column[j] == ''</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> break</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(1, seqNo):</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(1, seqNo):</span></span>
</pre>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> assert column[j] != '>' and column[j] != ''</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> column[j] = mapFn(column[j])</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> yield column[:]</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="p">@@ -878,8 +878,8 @@</span> def fastaAlignmentWrite(columnAlignment,</span>
</pre>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> Writes out column alignment to given file multi-fasta format</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> """</span>
</pre>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> fastaFile = open(fastaFile, 'w')</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- columnAlignment = [ i for i in columnAlignment if filter(i) ]</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for seq in xrange(0, seqNo):</span></span>
</pre>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ columnAlignment = [ i for i in columnAlignment if list(filter(i)) ]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for seq in range(0, seqNo):</span></span>
</pre>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> fastaFile.write(">%s\n" % names[seq])</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> for column in columnAlignment:</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> fastaFile.write(column[seq])</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="p">@@ -890,10 +890,10 @@</span> def getRandomSequence(length=500):</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> """Generates a random name and sequence.</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> """</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> fastaHeader = ""</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(int(random.random()*100)):</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(int(random.random()*100)):</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> fastaHeader = fastaHeader + random.choice([ 'A', 'C', '0', '9', ' ', '\t' ])</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> return (fastaHeader, \</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;">- "".join([ random.choice([ 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'N' ]) for i in xrange((int)(random.random() * length))]))</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ "".join([ random.choice([ 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'C', 'T', 'G', 'N' ]) for i in range((int)(random.random() * length))]))</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> </span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> def _expLength(i=0, prob=0.95):</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> if random.random() >= prob:</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="p">@@ -932,7 +932,7 @@</span> def reverseComplementChar(x):</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> _reverseComplementDict else x</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"> def reverseComplement(seq):</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return "".join(map(lambda x : reverseComplementChar(x), seq[::-1]))</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return "".join([reverseComplementChar(x) for x in seq[::-1]])</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> </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"> #########################################################</span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -1044,9 +1044,9 @@</span> def pWMRead(fileHandle, alphabetSize=4):</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> for line in lines[1:]:</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> l2 = [ float(i) for i in line.split() ]</span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> assert len(l) == len(l2)</span>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, len(l)):</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, len(l)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> l[i].append(l2[i])</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, len(l)):</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, len(l)):</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> j = sum(l[i]) + 0.0</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> l[i] = [ k/j for k in l[i] ]</span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> return l</span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="p">@@ -1054,8 +1054,8 @@</span> def pWMRead(fileHandle, alphabetSize=4):</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> def pWMWrite(fileHandle, pWM, alphabetSize=4):</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> """Writes file in standard PWM format, is reverse of pWMParser</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> """</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, alphabetSize):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fileHandle.write("%s\n" % ' '.join([ str(pWM[j][i]) for j in xrange(0, len(pWM)) ]))</span></span>
</pre>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, alphabetSize):</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fileHandle.write("%s\n" % ' '.join([ str(pWM[j][i]) for j in range(0, len(pWM)) ]))</span></span>
</pre>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> </span>
</pre>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> #########################################################</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> #########################################################</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"><span class="p">@@ -1230,8 +1230,8 @@</span> def cigarWrite(fileHandle, pairwiseAlign</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> def _getRandomSegment():</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"> contig = random.choice([ "one", "two", "three", "four" ])</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- start = random.choice(xrange(0, 10000))</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- end = start + random.choice(xrange(0, 1000))</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ start = random.choice(range(0, 10000))</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ end = start + random.choice(range(0, 1000))</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> strand = random.choice([ True, False ])</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> if not strand:</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> start, end = end, start</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="p">@@ -1245,7 +1245,7 @@</span> def getRandomOperationList(xLength, yLen</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> if operationMaxLength == 1:</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> length = 1</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> else:</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- length = random.choice(xrange(1, operationMaxLength))</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ length = random.choice(range(1, operationMaxLength))</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> if opType != PairwiseAlignment.PAIRWISE_INDEL_Y and xLength - length < 0:</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> continue</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> if opType != PairwiseAlignment.PAIRWISE_INDEL_X and yLength - length < 0:</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="p">@@ -1263,7 +1263,7 @@</span> def getRandomPairwiseAlignment():</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> """</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> i, j, k, l = _getRandomSegment()</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> m, n, o, p = _getRandomSegment()</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- score = random.choice(xrange(-1000, 1000))</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ score = random.choice(range(-1000, 1000))</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> return PairwiseAlignment(i, j, k, l, m, n, o, p, score, getRandomOperationList(abs(k - j), abs(o - n)))</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> #########################################################</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/misc.py</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/misc.py</span></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC215" 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="LC216" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/nxnewick.py</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/nxnewick.py</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -1,9 +1,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC223" 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="LC224" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"> #Copyright (C) 2006-2012 by Glenn Hickey</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> #Released under the MIT license, see LICENSE.txt</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> """read and write newick trees to and from networkx graphs (as wrapped by nxtree). </span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="p">@@ -14,7 +13,7 @@</span> import math</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"> import random</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> from string import whitespace as ws</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> from sonLib.misc import close</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import bioio</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import bioio</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> import networkx as NX</span>
</pre>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> from optparse import OptionParser</span>
</pre>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> from sonLib.nxtree import NXTree</span>
</pre>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="p">@@ -187,15 +186,15 @@</span> def main():</span>
</pre>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> parser.parseFile(args[0])</span>
</pre>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> NX.drawing.nx_agraph.write_dot(parser.nxTree.nxDg, args[1])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> parser.writeFile(args[2])</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "PRE"</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("PRE")</span></span>
</pre>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> for i in parser.nxTree.preOrderTraversal():</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("%d %s" % (i, parser.nxTree.getName(i)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "POST"</span></span>
</pre>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("%d %s" % (i, parser.nxTree.getName(i))))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("POST")</span></span>
</pre>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> for i in parser.nxTree.postOrderTraversal():</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("%d %s" % (i, parser.nxTree.getName(i)))</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "BFS"</span></span>
</pre>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("%d %s" % (i, parser.nxTree.getName(i))))</span></span>
</pre>
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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 class="gi" style="color: #000; background-color: #dfd;">+ print("BFS")</span></span>
</pre>
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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"> for i in parser.nxTree.breadthFirstTraversal():</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ("%d %s" % (i, parser.nxTree.getName(i)))</span></span>
</pre>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(("%d %s" % (i, parser.nxTree.getName(i))))</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> return 0</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"> </span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> if __name__ == '__main__': </span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/nxtree.py</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/nxtree.py</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="p">@@ -1,9 +1,8 @@</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> </span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> #Copyright (C) 2006-2012 by Glenn Hickey</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> #</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> #Released under the MIT license, see LICENSE.txt</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"> </span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> """A more general (ie arbitrary degree) tree to replace the BinaryTree</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> in sonLib.tree.py. Implemented as a lightweight wrapper over a </span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/allTests.py</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/allTests.py</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> </span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/bioioTest.py</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/bioioTest.py</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC288" 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="LC289" class="line" lang="diff"> </span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="p">@@ -61,12 +61,12 @@</span> class TestCase(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> #########################################################</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> </span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> def testTempFileTree(self):</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(100): #self.testNo):</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- levels = random.choice(xrange(1, 4))</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fileNo = random.choice(xrange(1, 6))</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(100): #self.testNo):</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ levels = random.choice(range(1, 4))</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fileNo = random.choice(range(1, 6))</span></span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> maxTempFiles = int(math.pow(fileNo, levels))</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> </span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "Got %s levels, %s fileNo and %s maxTempFiles" % (levels, fileNo, maxTempFiles)</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;">+ print("Got %s levels, %s fileNo and %s maxTempFiles" % (levels, fileNo, maxTempFiles))</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"> tempFileTreeRootDir = os.path.join(self.tempDir, getRandomAlphaNumericString())</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> tempFileTree = TempFileTree(tempFileTreeRootDir, fileNo, levels)</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">@@ -74,7 +74,7 @@</span> class TestCase(unittest.TestCase):</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"> tempFiles = []</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"> tempDirs = []</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> #Check we can mac number of temp files.</span>
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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(maxTempFiles):</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 i in range(maxTempFiles):</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"> if random.random() > 0.5:</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> tempFile = tempFileTree.getTempFile()</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> assert os.path.isfile(tempFile)</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="p">@@ -132,9 +132,9 @@</span> class TestCase(unittest.TestCase):</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"> def testFastaReadWrite(self):</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> tempFile = getTempFile()</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> self.tempFiles.append(tempFile)</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 test in xrange(0, self.testNo):</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fastaNumber = random.choice(xrange(10))</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- l = [ getRandomSequence() for i in xrange(fastaNumber) ]</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastaNumber = random.choice(range(10))</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ l = [ getRandomSequence() for i in range(fastaNumber) ]</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> fileHandle = open(tempFile, 'w')</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> for name, seq in l:</span>
</pre>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> fastaWrite(fileHandle, name, seq)</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="p">@@ -150,9 +150,9 @@</span> class TestCase(unittest.TestCase):</span>
</pre>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> def testFastqReadWrite(self):</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> tempFile = getTempFile()</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> self.tempFiles.append(tempFile)</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fastaNumber = random.choice(xrange(10))</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fastqs = [ (name, seq, [ random.randint(33, 126) for i in range(len(seq)) ]) for name, seq in [ getRandomSequence() for i in xrange(fastaNumber) ]]</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastaNumber = random.choice(range(10))</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastqs = [ (name, seq, [ random.randint(33, 126) for i in range(len(seq)) ]) for name, seq in [ getRandomSequence() for i in range(fastaNumber) ]]</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> fH = open(tempFile, 'w')</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> for name, seq, quals in fastqs:</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> fastqWrite(fH, name, seq, quals)</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="p">@@ -170,9 +170,9 @@</span> class TestCase(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> self.tempFiles.append(tempFile)</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> tempFile2 = getTempFile()</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> self.tempFiles.append(tempFile2)</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fastaNumber = random.choice(xrange(10))</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- l = [ getRandomSequence() for i in xrange(fastaNumber) ]</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastaNumber = random.choice(range(10))</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ l = [ getRandomSequence() for i in range(fastaNumber) ]</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> fileHandle = open(tempFile, 'w')</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"> for name, seq in l:</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> fastaWrite(fileHandle, name, seq)</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="p">@@ -180,7 +180,7 @@</span> class TestCase(unittest.TestCase):</span>
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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"> command = "sonLib_fastaCTest %s %s" % (tempFile, tempFile2)</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> </span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print command</span></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(command)</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> </span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> system(command)</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"> </span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="p">@@ -205,12 +205,12 @@</span> class TestCase(unittest.TestCase):</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> d = '((human,baboon),chimp);'</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> e = newickTreeParser(d)</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"> f = printBinaryTree(e, False)</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print d, f</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(d, f)</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> assert d == f</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"> </span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> def testNewickTreeParser_UnaryNodes(self):</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> #tests with unary nodes </span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> tree = getRandomTreeString()</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> logger.debug("tree to try\t", tree)</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> tree2 = newickTreeParser(tree, reportUnaryNodes=True)</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="p">@@ -229,7 +229,7 @@</span> class TestCase(unittest.TestCase):</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"> def testPWMParser(self):</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"> tempFile = getTempFile()</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> self.tempFiles.append(tempFile)</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"> pWM = getRandomPWM()</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> </span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> fileHandle = open(tempFile, 'w')</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="p">@@ -240,7 +240,7 @@</span> class TestCase(unittest.TestCase):</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"> pWM2 = pWMRead(fileHandle)</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> fileHandle.close()</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> </span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, len(pWM)): </span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, len(pWM)): </span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> pWM[i] == pWM2[i]</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> </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"><span class="p">@@ -254,9 +254,9 @@</span> class TestCase(unittest.TestCase):</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> def testCigarReadWrite(self):</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> tempFile = getTempFile()</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> self.tempFiles.append(tempFile)</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cigarNumber = random.choice(xrange(10))</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- l = [ getRandomPairwiseAlignment() for i in xrange(cigarNumber) ]</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cigarNumber = random.choice(range(10))</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ l = [ getRandomPairwiseAlignment() for i in range(cigarNumber) ]</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> fileHandle = open(tempFile, 'w')</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> for cigar in l:</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"> cigarWrite(fileHandle, cigar)</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="p">@@ -292,10 +292,10 @@</span> def getRandomPWM(length=-1):</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"> if length == -1:</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> length = 1 + int(random.random()*10)</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"> def fn():</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- l = [ random.random()*100 for i in xrange(0, 4) ]</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ l = [ random.random()*100 for i in range(0, 4) ]</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"> i = sum(l)</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> return [ j/i for j in l ]</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return [ fn() for i in xrange(0, length) ]</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return [ fn() for i in range(0, length) ]</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> </span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"> if __name__ == '__main__':</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> unittest.main()</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/cigarsTest.py</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/cigarsTest.py</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> </span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"> #</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="p">@@ -36,9 +36,9 @@</span> class TestCase(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"> tempFile = getTempFile()</span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"> self.tempFiles.append(tempFile)</span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pairwiseAlignmentNumber = random.choice(xrange(10))</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- l = [ getRandomPairwiseAlignment() for i in xrange(pairwiseAlignmentNumber) ]</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pairwiseAlignmentNumber = random.choice(range(10))</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ l = [ getRandomPairwiseAlignment() for i in range(pairwiseAlignmentNumber) ]</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"> fileHandle = open(tempFile, 'w')</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"> keepProbs = random.random() > 0.5</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/kvdbTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/kvdbTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC450" 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="LC451" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/nxnewickTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/nxnewickTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC458" 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="LC459" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"> #Copyright (C) 011 by Glenn Hickey</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"> #</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/nxtreeTest.py</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/nxtreeTest.py</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" 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="LC467" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"> #Copyright (C) 011 by Glenn Hickey</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/sonLib_daemonize.py</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/sonLib_daemonize.py</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<pre style="margin: 0;">+<span id="LC474" 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="LC475" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"> # Glenn Hickey 2011</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"> #</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="p">@@ -66,7 +66,7 @@</span> else:</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"> if __name__ == '__main__':</span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"> if len(sys.argv) != 2:</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Exception, "%s: Wrong number of arguments" % sys.argv[0]</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise Exception("%s: Wrong number of arguments" % sys.argv[0])</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"> pid = os.fork()</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"> if pid > 0:</span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/treeTest.py</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/treeTest.py</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"> </span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"><span class="p">@@ -29,29 +29,29 @@</span> class TestCase(unittest.TestCase):</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"> unittest.TestCase.tearDown(self)</span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"> </span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> def testRemodelTreeRemovingRoot(self):</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"> binaryTree = getRandomTree()</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> binaryTree_depthFirstNumbers(binaryTree) </span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> node = getRandomLeafNode(binaryTree)</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> remodTree = remodelTreeRemovingRoot(binaryTree, node.traversalID.mid)</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;">- print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)</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;">+ print("test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True))</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"> binaryTree_depthFirstNumbers(remodTree)</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"> distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"> d = getDistancesBetweenLeaves(binaryTree)</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"> d2 = getDistancesBetweenLeaves(remodTree)</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print d</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print d2</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(d)</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;">+ print(d2)</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"> for key in d2:</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"> assert close(d2[key], d[key], 0.0001)</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"> </span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"> def testMoveRoot(self):</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"> binaryTree = getRandomTree()</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"> binaryTree_depthFirstNumbers(binaryTree)</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"> node = getRandomNode(binaryTree)</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "before", printBinaryTree(binaryTree, True), printBinaryTree(node, True)</span></span>
</pre>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("before", printBinaryTree(binaryTree, True), printBinaryTree(node, True))</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"> remodTree = moveRoot(binaryTree, node.traversalID.mid)</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True)</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("test", test, printBinaryTree(binaryTree, True), printBinaryTree(node, True), printBinaryTree(remodTree, True))</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"> binaryTree_depthFirstNumbers(remodTree)</span>
</pre>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"> #distances = mapTraversalIDsBetweenTrees(binaryTree, remodTree)</span>
</pre>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"> #d = getDistancesBetweenLeaves(binaryTree)</span>
</pre>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="p">@@ -62,7 +62,7 @@</span> class TestCase(unittest.TestCase):</span>
</pre>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"> # assert close(d2[key], d[key], 0.0001)</span>
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534
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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"> def testCalculateDupsAndLossesByReconcilingTrees(self):</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"> speciesTree = getRandomTree()</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"> binaryTree_depthFirstNumbers(speciesTree)</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"> geneTree = getRandomTree()</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="p">@@ -102,13 +102,13 @@</span> class TestCase(unittest.TestCase):</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"> geneStrings = [ geneString1, geneString2, geneString3, geneString4, \</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"> geneString5, geneString6, geneString7, geneString8,</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"> geneString9, geneString10, geneString11 ]</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print ""</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("")</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"> for geneString, dupCount, lossCount in geneStrings:</span>
</pre>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"> geneTree = newickTreeParser(geneString)</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"> binaryTree_depthFirstNumbers(geneTree)</span>
</pre>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print printBinaryTree(geneTree, True), printBinaryTree(speciesTree, True)</span></span>
</pre>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(printBinaryTree(geneTree, True), printBinaryTree(speciesTree, True))</span></span>
</pre>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"> dupCount2, lossCount2 = calculateDupsAndLossesByReconcilingTrees(speciesTree, geneTree, processID=lambda x : x)</span>
</pre>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print geneString, "dups", dupCount, dupCount2, "losses", lossCount, lossCount2</span></span>
</pre>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(geneString, "dups", dupCount, dupCount2, "losses", lossCount, lossCount2)</span></span>
</pre>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"> assert dupCount == dupCount2</span>
</pre>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"> assert lossCount == lossCount2</span>
</pre>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"> </span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="p">@@ -144,11 +144,11 @@</span> class TestCase(unittest.TestCase):</span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> rootedGeneTree = newickTreeParser(geneString)</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"> binaryTree_depthFirstNumbers(geneTree)</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"> rootedGeneTree2, dupCount, lossCount = calculateProbableRootOfGeneTree(speciesTree, geneTree)</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "rootedGeneTree", rootedGeneString, dupCount, lossCount, printBinaryTree(rootedGeneTree2, False)</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("rootedGeneTree", rootedGeneString, dupCount, lossCount, printBinaryTree(rootedGeneTree2, False))</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"> #assert printBinaryTree(rootedGeneTree, False) == printBinaryTree(rootedGeneTree2, False)</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"> </span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"> def testCalculateProbableRootOfGeneTree(self):</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for test in xrange(0, self.testNo):</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for test in range(0, self.testNo):</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"> speciesTree = getRandomTree()</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"> binaryTree_depthFirstNumbers(speciesTree)</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"> geneTree = getRandomTree()</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/test/unitTest.py</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/test/unitTest.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="p">@@ -1,4 +1,4 @@</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"> </span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> #</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/sonLib/tree.py</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/sonLib/tree.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="p">@@ -1,4 +1,4 @@</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/env python3</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"> </span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"> #Copyright (C) 2006-2012 by Benedict Paten (benedictpaten@gmail.com)</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"> #</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="p">@@ -69,7 +69,7 @@</span> def binaryTree_depthFirstNumbers(binaryT</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"> return mid+1, leafNo+1</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> traverse(binaryTree)</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"> if labelTree:</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;">- for binaryTree in traversalIDs.keys():</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;">+ for binaryTree in list(traversalIDs.keys()):</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"> binaryTree.traversalID = traversalIDs[binaryTree]</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"> return traversalIDs</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"> </span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="p">@@ -164,18 +164,18 @@</span> def transformByDistance(wV, subModel, al</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"> transform wV by given substitution matrix</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"> """</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"> nc = [0.0]*alphabetSize</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, alphabetSize):</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, alphabetSize):</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"> j = wV[i]</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"> k = subModel[i]</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for l in xrange(0, alphabetSize):</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for l in range(0, alphabetSize):</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"> nc[l] += j * k[l]</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"> return nc</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"> </span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"> def multiplyWV(wVX, wVY, alphabetSize=4):</span>
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<td class="diff-line-num new new_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return [ wVX[i] * wVY[i] for i in xrange(0, alphabetSize) ]</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return [ wVX[i] * wVY[i] for i in range(0, alphabetSize) ]</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"> </span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"> def sumWV(wVX, wVY, alphabetSize=4):</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return [ wVX[i] + wVY[i] for i in xrange(0, alphabetSize) ]</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return [ wVX[i] + wVY[i] for i in range(0, alphabetSize) ]</span></span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"> </span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"> def normaliseWV(wV, normFac=1.0):</span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"> """</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="p">@@ -187,7 +187,7 @@</span> def normaliseWV(wV, normFac=1.0):</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"> def sumWVA(wVA, alphabetSize=4):</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"> totals = [0.0]*alphabetSize</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"> for wV in wVA:</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, alphabetSize):</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, alphabetSize):</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"> totals[i] += wV[i]</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"> return totals</span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"> </span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="p">@@ -222,7 +222,7 @@</span> def felsensteins(binaryTree, subMatrices</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"> def calculateCharacterFrequencies(seq, map, alphabetSize):</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"> counts = [0.0]*alphabetSize</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"> for i in seq:</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- counts[map(i)] += 1</span></span>
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ counts[list(map(i))] += 1</span></span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"> return counts</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"> </span>
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637
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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"><span class="p">@@ -261,9 +261,9 @@</span> def calculateDNADistanceMatrix(seqNo, fa</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"> transversions = [0.1]*seqNo*seqNo</span>
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"> counts = [1.0]*seqNo*seqNo</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"> for column in fastaIter:</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, seqNo):</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, seqNo):</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"> if column[i] in [ 'A', 'C', 'T', 'G' ]:</span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(i+1, seqNo):</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(i+1, seqNo):</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"> if column[j] in [ 'A', 'C', 'T', 'G' ]:</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"> counts[i*seqNo + j] += 1</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"> if column[i] != column[j]:</span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="p">@@ -277,9 +277,9 @@</span> def calculateDNADistanceMatrix(seqNo, fa</span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"> transversions[i*seqNo + j] += 1</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"> else:</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="diff"> transitions[i*seqNo + j] += 1</span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- distanceMatrix = [ [None]*seqNo for i in xrange(0, seqNo) ]</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, seqNo*seqNo):</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(i+1, seqNo):</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ distanceMatrix = [ [None]*seqNo for i in range(0, seqNo) ]</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, seqNo*seqNo):</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(i+1, seqNo):</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="diff"> k = i * seqNo + j</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="diff"> distanceMatrix[i][j] = -0.75*math.log(1 - (4/3)*((transitions[k]+transversions[k])/counts[k])) #jukes cantor correction</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"> distanceMatrix[j][i] = distanceMatrix[i][j]</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="p">@@ -288,10 +288,10 @@</span> def calculateDNADistanceMatrix(seqNo, fa</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"> return distanceMatrix</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"> </span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="diff"> def makeDistancePairs(distanceMatrix, iDs, seqNo):</span>
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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- binaryTrees = [ BinaryTree(0.0, False, None, None, iDs[i]) for i in xrange(0, seqNo) ]</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ binaryTrees = [ BinaryTree(0.0, False, None, None, iDs[i]) for i in range(0, seqNo) ]</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"> distancePairs = []</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;">- for i in xrange(0, seqNo):</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(i+1, seqNo): </span></span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, seqNo):</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(i+1, seqNo): </span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"> distancePairs.append(DistancePair(distanceMatrix[i][j], binaryTrees[i], 1, binaryTrees[j], 1))</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> distancePairs.append(DistancePair(distanceMatrix[i][j], binaryTrees[j], 1, binaryTrees[i], 1))</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"> return distancePairs</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="p">@@ -327,10 +327,10 @@</span> def upgmaI(distancePairs, leafNo):</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"> holder1[i.leaf2] = i</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> if i.leaf1 == distancePair.leaf2 and i.leaf2 != distancePair.leaf1:</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> holder2[i.leaf2] = i</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert len(holder1.keys()) == leafNo-2</span></span>
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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;">- assert len(holder2.keys()) == leafNo-2</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;">+ assert len(list(holder1.keys())) == leafNo-2</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert len(list(holder2.keys())) == leafNo-2</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> assert set(holder1.keys()) == set(holder2.keys())</span>
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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;">- for i in holder1.keys():</span></span>
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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;">+ for i in list(holder1.keys()):</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> j = holder1[i]</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> k = holder2[i]</span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> newDistance = (j.distance*j.leafNo1 + k.distance*k.leafNo1)/(j.leafNo1 + k.leafNo1)</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="p">@@ -346,7 +346,7 @@</span> def nj(distanceMatrix, iDs, leafNo):</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"> </span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"> def getMinPair(distancePairs, rValues, leafNo):</span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"> j = None</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;">- k = sys.maxint</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;">+ k = sys.maxsize</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"> for i in distancePairs:</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"> adjustD = i.distance - (rValues[i.leaf1] + rValues[i.leaf2])/(leafNo-2)</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"> #print "the adjusted value ", adjustD, i.distance, rValues[i.leaf1]/(leafNo-2), rValues[i.leaf2]/(leafNo-2)</span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"><span class="p">@@ -359,11 +359,11 @@</span> def getMinPair(distancePairs, rValues, l</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"> def calculateRValues(distancePairs, leafNo):</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> j = {}</span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"> for i in distancePairs:</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if j.has_key(i.leaf1):</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if i.leaf1 in j:</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"> j[i.leaf1] += i.distance</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"> else:</span>
</pre>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"> j[i.leaf1] = i.distance</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert len(j.keys()) == leafNo</span></span>
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<td class="diff-line-num new new_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert len(list(j.keys())) == leafNo</span></span>
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<td class="diff-line-num new new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"> return j</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"> def njI(distancePairs, leafNo):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="p">@@ -391,10 +391,10 @@</span> def njI(distancePairs, leafNo):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"> holder1[i.leaf2] = i</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"> if i.leaf1 == distancePair.leaf2 and i.leaf2 != distancePair.leaf1:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"> holder2[i.leaf2] = i</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert len(holder1.keys()) == leafNo-2</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assert len(holder2.keys()) == leafNo-2</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert len(list(holder1.keys())) == leafNo-2</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assert len(list(holder2.keys())) == leafNo-2</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"> assert set(holder1.keys()) == set(holder2.keys())</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in holder1.keys():</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in list(holder1.keys()):</span></span>
</pre>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"> j = holder1[i]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"> k = holder2[i]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"> assert j.leaf2 == k.leaf2</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="p">@@ -416,13 +416,13 @@</span> def njI(distancePairs, leafNo):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"> def checkMatrix(m, fV, AS=4, reversible=True):</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"> #print m</span>
</pre>
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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"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, AS):</span></span>
</pre>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, AS):</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"> j = sum(m[i])</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"> #print "AAAAA", j</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"> assert j <= 1.0001</span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"> assert j >= 0.9999</span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"> if reversible:</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="gd" style="color: #000; background-color: #fdd;">- for k in xrange(0, AS):</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k in range(0, AS):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"> #print "comp2", (fV[i] * m[i][k]), (fV[k] * m[k][i] )</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"> assert close(fV[i] * m[i][k], fV[k] * m[k][i], 0.00001)</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"><span class="p">@@ -436,9 +436,9 @@</span> def checkMatrix(m, fV, AS=4, reversible=</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"> assert close(i, j, 0.00001)</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"> </span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"> def reverseSubMatrix(m, AS=4):</span>
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<td class="diff-line-num new new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- k = [ [None]*AS for i in xrange(0, AS) ]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, AS):</span></span>
</pre>
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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;">- for j in xrange(0, AS):</span></span>
</pre>
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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;">+ k = [ [None]*AS for i in range(0, AS) ]</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, AS):</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(0, AS):</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"> k[j][i] = m[i][j]</span>
</pre>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"> return k</span>
</pre>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"> </span>
</pre>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"><span class="p">@@ -476,7 +476,7 @@</span> def subMatrix_TamuraNei(d, fA, fC, fG, f</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"> AS = 4</span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"> freq = ( fA, fC, fG, fT )</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"> alpha = ( alphaPur, alphaPyr, alphaPur, alphaPyr )</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix = [ [ 0.0 ]*AS for i in xrange(0, AS) ]</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix = [ [ 0.0 ]*AS for i in range(0, AS) ]</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"> #see page 203 of Felsenstein's Inferring Phylogenies for explanation of calculations</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"> def watKro(j, k):</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"> if (j % 2) == (k % 2):</span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"><span class="p">@@ -486,10 +486,10 @@</span> def subMatrix_TamuraNei(d, fA, fC, fG, f</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"> if i == j:</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"> return 1.0</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"> return 0.0</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, AS): #long winded, totally unoptimised method for calculating matrix</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for j in xrange(0, AS):</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for i in range(0, AS): #long winded, totally unoptimised method for calculating matrix</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for j in range(0, AS):</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"> l = 0.0</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for k in xrange(0, AS):</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for k in range(0, AS):</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"> l += watKro(j, k) * freq[k]</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> matrix[i][j] =\</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"> math.exp(-(alpha[i] + beta) * d) * kroenickerDelta(i, j) + \</span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"><span class="p">@@ -516,9 +516,9 @@</span> def subMatrix_HKY(d, fA, fC, fG, fT, tra</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"> def subMatrix_HalpernBruno(d, freqColumn, subMatrix, AS=4):</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"> #return subMatrix_HKY(d, freqColumn[0], freqColumn[1], freqColumn[2], freqColumn[3], 2.0)</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"> #return subMatrix</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- matrix = [ [ 0.0 ]*AS for i in xrange(0, AS) ]</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for i in xrange(0, AS):</span></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;">- for j in xrange(0, AS):</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ matrix = [ [ 0.0 ]*AS for i in range(0, AS) ]</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;">+ for i in range(0, AS):</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;">+ for j in range(0, AS):</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"> a = freqColumn[i] * subMatrix[i][j]</span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"> b = freqColumn[j] * subMatrix[j][i]</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"> if not close(a, b, 0.0001):</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"><span class="p">@@ -580,8 +580,8 @@</span> def mapTraversalIDsBetweenTrees(oldTree,</span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"> internalMap[(fn(oldTree), fn(oldTree.left))] = fn(oldTree.right)</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"> internalMap[(fn(oldTree.left), fn(oldTree))] = fn(oldTree.right)</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"> fn3(oldTree)</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print leafMap</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print internalMap</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(leafMap)</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(internalMap)</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"> def fn4(newTree):</span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"> if newTree.internal:</span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"> fn4(newTree.left)</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="p">@@ -596,7 +596,7 @@</span> def remodelTreeRemovingRoot(root, node):</span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"> """</span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"> Node is mid order number</span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"> """</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import bioio</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import bioio</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"> assert root.traversalID.mid != node</span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"> hash = {}</span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"> def fn(bT):</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"><span class="p">@@ -632,7 +632,7 @@</span> def moveRoot(root, branch):</span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"> """</span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"> Removes the old root and places the new root at the mid point along the given branch</span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"> """</span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- import bioio</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from . import bioio</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"> if root.traversalID.mid == branch:</span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"> return bioio.newickTreeParser(bioio.printBinaryTree(root, True))</span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"> def fn2(tree, seq):</span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"><span class="p">@@ -703,7 +703,7 @@</span> def calculateDupsAndLossesByReconcilingT</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"> if nodes.issubset(a[speciesTree.right.traversalID.mid]):</span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"> return fn2(nodes, speciesTree.right)</span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"> return speciesTree.traversalID.mid</span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for iD in b.keys():</span></span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for iD in list(b.keys()):</span></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"> nodes = b[iD]</span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"> b[iD] = fn2(nodes, speciesTree)</span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"> dups = []</span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"><span class="p">@@ -725,7 +725,7 @@</span> def calculateDupsAndLossesByReconcilingT</span>
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"> nodes.append((node, losses+1))</span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"> return nodes</span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"> for node, losses in fn4(speciesTree):</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;">- lossMap[(sys.maxint, node)] = losses+1</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;">+ lossMap[(sys.maxsize, node)] = losses+1</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"> losses = [0]</span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"> def fn5(geneTree, ancestor):</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"> if geneTree.internal:</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"><span class="p">@@ -745,7 +745,7 @@</span> def calculateDupsAndLossesByReconcilingT</span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"> if speciesTree.internal:</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"> fn6(speciesTree.left, speciesTree.traversalID.mid, node)</span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"> fn6(speciesTree.right, speciesTree.traversalID.mid, node)</span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ancestor = fn6(speciesTree, sys.maxint, b[geneTree.traversalID.mid])</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ancestor = fn6(speciesTree, sys.maxsize, b[geneTree.traversalID.mid])</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="diff"> assert ancestorHolder[0] is not None</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="diff"> fn5(geneTree, ancestorHolder[0])</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> return len(dups), losses[0]</span></pre>
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<li id="82e0bda1ef781bbe11386f41bc18524910c179a4">
<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#82e0bda1ef781bbe11386f41bc18524910c179a4"><strong>debian/patches/fix_test.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/C/Makefile</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/C/Makefile</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -65,4 +65,4 @@</span> ${libPath}/sonLib.a : ${libSources} ${cp</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> mv sonLib.a ${libPath}/</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> </span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> test:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- python3 allTests.py --testLength=SHORT --logLevel CRITICAL</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PYTHONPATH=../src/sonLib python3 allTests.py --testLength=SHORT --logLevel CRITICAL</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span> externalToolsP.clean :</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> cd externalTools && make clean</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> test : all</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PYTHONPATH=.. PATH=../../bin:$$PATH python3 allTests.py --testLength=SHORT --logLevel=CRITICAL</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PYTHONPATH=$(CURDIR)/src:$(CURDIR)/src/sonLib PATH=$(CURDIR)/bin:$$PATH python3 src/sonLib/test/allTests.py --testLength=SHORT --logLevel=CRITICAL</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> ${binPath}/sonLib_daemonize.py : sonLib_daemonize.py</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> cp sonLib_daemonize.py ${binPath}/sonLib_daemonize.py</span></pre>
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<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_quicktree.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix_test.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#51664dd3d87bd8d260785cd9b786f636afb4c7dd"><strong>debian/patches/use_debian_packaged_quicktree.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: Tue, 16 Jun 2020 08:23:45 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: To avoid a code copy of quicktree here inside the quicktree</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> package a static lib is built and used to link here</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/externalTools/Makefile</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/externalTools/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -1,20 +1,14 @@</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,3 +29,37 @@</td>
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<pre style="margin: 0;"> <span id="LC29" 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="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-quicktreeM.clean :</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd quicktree_1.1 && make clean</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/C/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/C/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -7,12 +7,11 @@</span> cppSources = impl/*.cpp</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> libHeaders = $(wildcard inc/*.h)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> libInternalHeaders = impl/*.h</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> libTests = tests/sonLib*.c tests/st*</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-quickTreeObjects = ../externalTools/quicktree_1.1/obj/buildtree.o ../externalTools/quicktree_1.1/obj/cluster.o ../externalTools/quicktree_1.1/obj/distancemat.o ../externalTools/quicktree_1.1/obj/options.o ../externalTools/quicktree_1.1/obj/sequence.o ../externalTools/quicktree_1.1/obj/tree.o ../externalTools/quicktree_1.1/obj/util.o</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> quickTreeLibPath = ../externalTools/quicktree_1.1/include/</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> testProgs = ${binPath}/sonLibTests ${binPath}/sonLib_kvDatabaseTest ${binPath}/sonLib_cigarTest ${binPath}/sonLib_fastaCTest ${binPath}/sonLib_dynamicConnectivity_performance</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-cflags += ${tokyoCabinetIncl} ${kyotoTycoonIncl} ${tokyoTyrantIncl} ${mysqlIncl} ${pgsqlIncl} -I${quickTreeLibPath}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+cflags += ${tokyoCabinetIncl} ${kyotoTycoonIncl} ${tokyoTyrantIncl} ${mysqlIncl} ${pgsqlIncl} -I/usr/include/quicktree</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> cppflags += ${kyotoTycoonIncl}</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> all : ${libPath}/sonLib.a ${testProgs}</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="p">@@ -22,7 +21,7 @@</span> clean :</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> ${binPath}/sonLibTests : ${libTests} ${libInternalHeaders} ${libPath}/sonLib.a ${libPath}/cuTest.a tests/allTests.c</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> @mkdir -p $(dir $@)</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${cxx} ${cflags} -I inc -I ${libPath} -o $@.tmp tests/allTests.c ${libTests} ${libPath}/sonLib.a ${libPath}/cuTest.a ${dblibs} ${mysqlLibs} -lm -lstdc++ -lpthread</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${cxx} ${cflags} -I inc -I ${libPath} -o $@.tmp tests/allTests.c ${libTests} ${libPath}/sonLib.a ${libPath}/cuTest.a ${dblibs} ${mysqlLibs} -lm -lstdc++ -lpthread -lquicktree</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> mv $@.tmp $@</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> ${binPath}/sonLib_kvDatabaseTest : ${libTests} ${libInternalHeaders} ${libPath}/sonLib.a ${libPath}/cuTest.a tests/kvDatabaseTest.c tests/kvDatabaseTestCommon.c</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -60,7 +59,7 @@</span> ${libPath}/sonLib.a : ${libSources} ${cp</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> @mkdir -p $(dir $@)</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> ${cxx} ${cflags} -I inc -I ${libPath}/ -c ${libSources}</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> ${cpp} ${cppflags} -I inc -I ${libPath}/ -c ${cppSources}</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ar rc sonLib.a *.o ${quickTreeObjects}</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ar rc sonLib.a *.o</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> ranlib sonLib.a </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> rm *.o</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> mv sonLib.a ${libPath}/</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/libsonlib/-/compare/2fdf58ac24255692fccd10b4df734b2ee6304528...e02ce9f8e568331b7320aaad5855e7fa59c8b051#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">@@ -20,6 +20,12 @@ include /usr/share/dpkg/default.mk</td>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">%:</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> # Somehow Makefile does not deal with this ...</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> mkdir -p bin</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> cp -a src/sonLib/test/sonLib_daemonize.py .</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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23
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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24
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">#override_dh_auto_test:</span>
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25
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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