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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/550bc0485e6922c701abb50c567c66b67f7ddd0c">550bc048</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-25T14:06:38Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/0d5a5400614659b27b8174f8fbdc4e2e637526d0">0d5a5400</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-25T14:06:39Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.8+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/6e240027179cbf974842358170d8a3cce2745494">6e240027</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-25T14:06:40Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/6.0.8+dfsg'

Update to upstream version '6.0.8+dfsg'

with Debian dir 3684c6515cc70e01ee07fbaa5ac4e2f25bf5c627</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/29a4a8e8386166751e9995a5519ece1ea9402cf1">29a4a8e8</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-25T14:36:05Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix changelog, drop Debian craftet 2to3 patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/745fb586ec901fe636041b7645c31d2567c6a723">745fb586</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-25T14:36:44Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends: python3

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/58febd44dee1173453570bf278e2c9becac5b423">58febd44</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-25T14:38:25Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix perl interpreter path

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/49bbba390194d4ec62008d2ef6dcf58ea36447af">49bbba39</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-25T14:41:46Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>12 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#587d266bb27a4dc3022bbed44dfa19849df3044c">

.gitlab-ci.yml

</a>

</li>

<li class="file-stats">

<a href="#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

CHANGELOG

</a>

</li>

<li class="file-stats">

<a href="#ff6936350384213d6f693f4d604134188ce088c8">

CHANGEUID

</a>

</li>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">

<span class="deleted-file">

−

debian/patches/2to3.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<span class="deleted-file">

−

debian/patches/series

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

<li class="file-stats">

<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">

proteinortho6.pl

</a>

</li>

<li class="file-stats">

<a href="#e52fa9f6246a270e3b0a6a888a797d22f02e2532">

src/proteinortho_ffadj_mcs.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="587d266bb27a4dc3022bbed44dfa19849df3044c">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#587d266bb27a4dc3022bbed44dfa19849df3044c"><strong>.gitlab-ci.yml</strong></a>

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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>

<td class="diff-line-num unfold js-unfold new_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>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,20 +17,17 @@ gcc-latest-alloptions:</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">tar xzf diamond-linux64.tar.gz</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir ~/bin</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp diamond ~/bin</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">perl proteinortho*pl -project=testasd -cpus=1 -ram=100 -verbose=2 -selfblast -silent -force -desc -checkfasta -cleanblast -debug -binpath=~/bin -tmp='~/' -e=0.000001 -sim=0.9 -identity=20 -cov=30 -subparaBlast='--more-sensitive' -synteny -dups=1 -cs=4 -alpha=0.4 -conn=0.01 -purity=0.00001 -minspecies=2 -subparaCluster='-cpus 1 -seed 1' -nograph -singles -xml -exactstep3 test/*faa >/dev/null 2>&1 && rm testasd*<span class="idiff left right">info* && export LC_NUMERIC="C" && export LC_ALL="C" && for f in testasd.*; do sort $f >$f.testasd; done; sha256sum -b *testasd | tr -d '\n' | awk '{if($0 == "eb88ba29afd4f2dba16d3dbf97a5b0d2ab7686654a854f8502f0e778628e7f56 *testasd.descriptions.testasd120f22094e2d6a75fb650523c7b5c2763a316aa7f8884dff0cbe3ccd002c9e1e *testasd.ffadj-graph.testasd9ad470e29be4937c6f4996f80221ede51670824bb2e4bb4a50946062a130ffd7 *testasd.poff.html.testasd4f8263bb4b2738e528635f3e121c659407119a1aecafb5340c9d28f5bd66cdaf *testasd.poff.tsv.testasd26d7f5d7b87dd7b71b4920753dc65e7c303e89cdfa56d3aaf00033c7918e6d10 *testasd.poff.tsv.xml</span>.testasdf80df4c1a951bfb55b02300a273f6395694f01e8ae908e296d9c14a847d432ac *testasd.proteinortho.html.testasdfa18e9a0530f5a5754f045cfe97deaf818bdb5eb725619952633f1da0641cf7b *testasd.proteinortho.tsv.testasdc598b8c43e48e06614ec19e2f6b870e2737a7117a50ab2b1613880764d0884b2 *testasd.proteinortho.tsv.xml.testasd"){print $0." -> OK"; exit 0}else{print $0." -> failed"; exit 1}}'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(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="LC20" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">perl proteinortho*pl -project=testasd -cpus=1 -ram=100 -verbose=2 -selfblast -silent -force -desc -checkfasta -cleanblast -debug -binpath=~/bin -tmp='~/' -e=0.000001 -sim=0.9 -identity=20 -cov=30 -subparaBlast='--more-sensitive' -synteny -dups=1 -cs=4 -alpha=0.4 -conn=0.01 -purity=0.00001 -minspecies=2 -subparaCluster='-cpus 1 -seed 1' -nograph -singles -xml -exactstep3 test/*faa >/dev/null 2>&1 && rm testasd*<span class="idiff left right">poff* && rm testasd*fadj* && rm testasd*info* && export LC_NUMERIC="C" && export LC_ALL="C" && for f in testasd.*; do sort $f >$f.testasd; done; sha256sum -b *testasd | tr -d '\n' | awk '{if($0 == "eb88ba29afd4f2dba16d3dbf97a5b0d2ab7686654a854f8502f0e778628e7f56 *testasd.descriptions</span>.testasdf80df4c1a951bfb55b02300a273f6395694f01e8ae908e296d9c14a847d432ac *testasd.proteinortho.html.testasdfa18e9a0530f5a5754f045cfe97deaf818bdb5eb725619952633f1da0641cf7b *testasd.proteinortho.tsv.testasdc598b8c43e48e06614ec19e2f6b870e2737a7117a50ab2b1613880764d0884b2 *testasd.proteinortho.tsv.xml.testasd"){print $0." -> OK"; exit 0}else{print $0." -> failed"; exit 1}}'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"><span class="na" style="color: #008080;">gcc-latest-all-p</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml">  <span class="na" style="color: #008080;">image</span><span class="pi">:</span> <span class="s" style="color: #d14;">gcc</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml">  <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">recompile-and-test</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml">  <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;">#- apt-get -y install libboost-all-dev</span></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">export CWD=$(pwd)</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">echo "installing last"</span></span>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">wget http://last.cbrc.jp/last-982.zip && unzip last*zip 2>/dev/null && cd last*/ && make && cp src/last* $HOME</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing usearch"</span></span>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">curl https://drive5.com/cgi-bin/upload3.py?license=2019070410321731111 --output $HOME/usearch && chmod +x $HOME/usearch</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;">#- echo "installing rapsearch"</span></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml">  <span class="c1" style="color: #998; font-style: italic;">#- git clone https://github.com/zhaoyanswill/RAPSearch2 && cd RAP*/Src && make && mv *rapsearch* $HOME && cd ../../ </span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing mmseqs2"</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">git clone https://github.com/soedinglab/MMseqs2 && cd MMs* && cmake . && make && cp src/mmseqs $HOME && cd ..</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cd $CWD && echo "installing blat"</span></span>

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<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="221" 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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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext">    updated shebang of ffadj such that python2.7 is used directly (ffadj fails if called with higher version of python)</span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext">    -p=blastp is now alias of blastp+ and legacy blast is now -p=blastp_legacy (blastn is equivalent)</span>

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<td class="diff-line-num old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext">    Makefile: static now includes -lquadmath</span>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(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="LC224" class="line" lang="plaintext">    25. Sept (uid: 3899)</span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">    synteny update to python3 (but the code looks fishy, the -synteny option now gets a deprecated warning)</span>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">    proteinortho now only print html for <10 files automatically and otherwise only gives the option</span></pre>

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<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">38<span class="idiff left right">13</span></span></pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">38<span class="idiff left right">99</span></span></pre>

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</li>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>

<hr>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make' for compiling everything in the current directory (using the installed version of lapack in e.g. /usr/lib/, you can install lapack with e.g. apt-get install libatlas3-base or liblapack3)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make STATIC=TRUE' for a static version</span></span>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make USELAPACK=FALSE' for a version without(!) LAPACK (only power iteration is used)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make USEPRECOMPILEDLAPACK=FALSE' for directly recompiling the provided lapack version 3.8.0 and linking dynamically<span class="idiff left right"> </span></span></span>

</pre>

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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="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make USEPRECOMPILEDLAPACK=FALSE' for directly recompiling the provided lapack version 3.8.0 and linking dynamically</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make CXX=g++-7' for using the g++-7 compiler. See Flags below for more informations</span></span>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make CXX=clang++' for using the clang compiler<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make CXX=clang++' for using the clang compiler</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make install' for installing the compiled files to /usr/local/bin</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Run 'make install PREFIX=/home/paul/bin/' for local installation</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">############ <span class="idiff left right">FLAG</span>S: ##########################################</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">############ <span class="idiff left right">OPTION</span>S: ##########################################</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## STATIC=TRUE : enable static compiling (default:FALSE) </span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## CXX=g++ : the g++ compiler</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## CXXFLAGS = compiler flags passed to g++</span></span>

</pre>

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19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## CXXLIBRARY = the path to the libs like lapack,... (dont forget the -L)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## CXXINCLUDE = include path (^) (dont forget the -I)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## PREFIX = the installation prefix (only for make install)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">##############################################################</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">##############################################################<span class="idiff left right">##</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">##########################</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## enviroment variables ##</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="32" 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">@@ -32,12 +32,24 @@ USELAPACK=TRUE</td>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># compile statically</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="nv" style="color: #008080;">STATIC</span><span class="o" style="font-weight: 600;">=</span>FALSE</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(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="LC35" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">static</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"><span class="nv" style="color: #008080;">STATIC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(static)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(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="LC37" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">PREFIX</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" 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">

36

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nv" style="color: #008080;">INSTALLDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(PREFIX)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">prefix</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="make"><span class="nv" style="color: #008080;">INSTALLDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(prefix)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

44

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">installdir</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

45

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="make"><span class="nv" style="color: #008080;">INSTALLDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(installdir)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

46

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" 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">

38

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<td class="diff-line-num new_line" data-linenumber="47" 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">

47

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC47" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">LAPACK</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" 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">

39

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<td class="diff-line-num new_line" data-linenumber="48" 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">

48

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC48" class="line" lang="make"><span class="nv" style="color: #008080;">USELAPACK</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(LAPACK)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" 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">

40

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<td class="diff-line-num new_line" data-linenumber="49" 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">

49

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC49" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(STATIC),true)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC51" class="line" lang="make"><span class="nv" style="color: #008080;">STATIC</span><span class="o" style="font-weight: 600;">=</span>TRUE</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" 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">

41

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<td class="diff-line-num new_line" data-linenumber="53" 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">

53

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" 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">

42

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<td class="diff-line-num new_line" data-linenumber="54" 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">

54

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make"><span class="nv" style="color: #008080;">USEPRECOMPILEDLAPACK</span><span class="o" style="font-weight: 600;">=</span>TRUE</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="43" 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">

43

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<td class="diff-line-num new_line" data-linenumber="55" 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">

55

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC55" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="144" 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">@@ -132,7 +144,7 @@ ifeq ($(USELAPACK),TRUE)</td>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(USEPRECOMPILEDLAPACK),TRUE)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" 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">

133

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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">($(STATIC),TRUE)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="134" 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">

134

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<td class="diff-line-num new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@echo</span> <span class="s2" style="color: #d14;">"[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@$(CXX)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(CXXFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(CXXFLAGS_PO)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span>  <span class="err" style="color: #a61717; background-color: #e3d2d2;">-o</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$<</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDLIBS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-static</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--allow-multiple-definition</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-llapack</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lblas</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lgfortran</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-<span class="idiff left">lquadmath</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-pthread</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-Wl,--whole-archive</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-lpthread</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">-Wl,--no-whole-archive</span></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">([</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$?</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-eq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>

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<td class="diff-line-num new old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(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="LC147" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">@$(CXX)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(CXXFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(CXXFLAGS_PO)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span>  <span class="err" style="color: #a61717; background-color: #e3d2d2;">-o</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$<</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDLIBS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-static</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--allow-multiple-definition</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-llapack</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lblas</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lgfortran</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-<span class="idiff left">pthread</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-Wl,--whole-archive</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-lpthread</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">-Wl,--no-whole-archive</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">-lquadmath</span></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">([</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$?</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-eq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>

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136

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<td class="diff-line-num new_line" data-linenumber="148" 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">

148

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make">         <span class="err" style="color: #a61717; background-color: #e3d2d2;">echo</span> <span class="s2" style="color: #d14;">"......$(ORANGE)static linking failed, now I try dynamic linking.$(NC)"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>

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137

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<td class="diff-line-num new_line" data-linenumber="149" 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">

149

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="make">         <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(CXX)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(CXXFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(CXXFLAGS_PO)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-fopenmp</span>  <span class="err" style="color: #a61717; background-color: #e3d2d2;">-o</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$@</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$<</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDFLAGS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(LDLIBS)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-llapack</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lblas</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-pthread</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--whole-archive</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-lpthread</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-Wl,--no-whole-archive</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">([</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$$?</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-eq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">echo</span> <span class="s2" style="color: #d14;">"......OK dynamic linking was successful for proteinortho_clustering!"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>

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<td class="diff-line-num new_line" data-linenumber="150" 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">

150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="make">                 <span class="err" style="color: #a61717; background-color: #e3d2d2;">echo</span> <span class="s2" style="color: #d14;">"......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">;</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="228" 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">@@ -216,15 +228,15 @@ install: proteinortho6.pl proteinortho $(BUILDDIR)/proteinortho_extract_from_gra</td>

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<td class="diff-line-num old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="228" 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">

228

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"INSTALLING everything to </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="229" 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">

229

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-v</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="218" 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">

218

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<td class="diff-line-num new_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">Everything installed successfully to </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">.</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"If needed you can add </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;"> to </span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: #008080;">$PATH</span><span class="s2" style="color: #d14;"> with 'export PATH=</span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: #008080;">$PATH</span><span class="s2" style="color: #d14;">:</span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">'."</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"If needed you can add </span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;"> to </span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: #008080;">$PATH</span><span class="s2" style="color: #d14;"> with 'export PATH=</span><span class="se" style="color: #d14;">\$</span><span class="nv" style="color: #008080;">$PATH</span><span class="s2" style="color: #d14;">:</span><span class="nv" style="color: #008080;">$(INSTALLDIR)</span><span class="s2" style="color: #d14;">'."</span></span>

</pre>

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220

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232

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="233" 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">

233

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">test</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl test_<span class="idiff left right">step2 test_step3 test_clean</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

223

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<td class="diff-line-num new_line old" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[TEST] All tests </span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="idiff left right">       </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

234

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl test_<span class="idiff left right">clean test_step2 test_step3 test_clean2</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(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="LC235" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[TEST] All tests </span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">test_step2</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="make"><span class="nl">test_step2</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho6.pl</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped)"</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[TEST] 1. basic proteinortho6.pl -step=2 test. (algorithms that are not present are skipped)"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">" [1/12] -p=blastp+ test: "</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="s2" style="color: #d14;">which blastp</span><span class="nv" style="color: #008080;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="make">         <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">blastp missing, skipping...</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="246" 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">@@ -234,15 +246,15 @@ test_step2: proteinortho6.pl</td>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="make">         <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="247" 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">

247

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

237

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="make"> <span class="nl">@echo -n " [2/12] -p=blastp+ synteny (PoFF) test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

238

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="s2" style="color: #d14;">which blastp</span><span class="nv" style="color: #008080;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

239

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="make">         <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(ORANGE)</span><span class="s2" style="color: #d14;">blastp missing, skipping...</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

240

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="make"> <span class="k" style="font-weight: 600;">else</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

241

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="make">         ./proteinortho6.pl <span class="nt" style="color: #000080;">-silent</span> <span class="nt" style="color: #000080;">-force</span> <span class="nt" style="color: #000080;">-project</span><span class="o" style="font-weight: 600;">=</span>test_synteny <span class="nt" style="color: #000080;">-synteny</span> <span class="nt" style="color: #000080;">-singles</span> <span class="nt" style="color: #000080;">-p</span><span class="o" style="font-weight: 600;">=</span>blastp+ <span class="nb" style="color: #0086b3;">test</span>/<span class="k" style="font-weight: 600;">*</span>.faa<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

242

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="make">         <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span> <span class="p">;</span> ./src/chk_test.pl test_synteny.proteinortho.tsv<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

243

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="make">         <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span> <span class="p">;</span> ./src/chk_test.pl test_synteny.poff.tsv<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

244

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="make">         <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

245

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<td class="diff-line-num new_line old" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC245" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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">

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> @echo -n " [2/12] -p=blastp+ synteny (PoFF) test: "</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="250" style="width: 35px; color: rgba(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="LC250" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> @if [ "$(shell which blastp)" = "" ]; then\</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC251" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>         echo "$(ORANGE)blastp missing, skipping...$(NC)"; \</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> else \</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>         ./proteinortho6.pl -silent -force -project=test_synteny -synteny -singles -p=blastp+ test/*.faa; \</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC254" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>         set -e ; ./src/chk_test.pl test_synteny.proteinortho.tsv; \</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>         set -e ; ./src/chk_test.pl test_synteny.poff.tsv; \</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="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">

</td>

<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">

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>         echo "$(GREEN)passed$(NC)"; \</span></span>

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257

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<pre style="margin: 0;">+<span id="LC257" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right">#</span> fi</span></span>

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246

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258

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="make"></span>

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247

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259

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="make"> <span class="nl">@echo -n " [3/12] -p=diamond test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">"</span></span>

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248

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260

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="make"> <span class="p">@</span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="s2" style="color: #d14;">which diamond</span><span class="nv" style="color: #008080;">)</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span><span class="se" style="color: #d14;">\</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="361" 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">@@ -349,11 +361,16 @@ test_step3: proteinortho6.pl test_step2</td>

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361

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(GREEN)</span><span class="s2" style="color: #d14;">passed</span><span class="nv" style="color: #008080;">$(NC)</span><span class="s2" style="color: #d14;">"</span></span>

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362

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="make"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">test_clean</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="make"><span class="nl">test_clean</span><span class="o" style="font-weight: 600;">:</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

364

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="make"><span class="nl">test_clean</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="365" style="width: 35px; color: rgba(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="LC365" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[TEST] Clean up all test files..."</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

366

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> proteinortho_cache_test_<span class="k" style="font-weight: 600;">*</span> test.<span class="k" style="font-weight: 600;">*</span> test_<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/C.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/E.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/C2.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/L.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/M.faa.<span class="k" style="font-weight: 600;">*</span><span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

367

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<pre style="margin: 0;">+<span id="LC367" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="368" style="width: 35px; color: rgba(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="LC368" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">test_clean2</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="353" style="width: 35px; color: rgba(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="LC369" class="line" lang="make"><span class="nl">test_clean2</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="353" 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">

353

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<td class="diff-line-num new_line" data-linenumber="370" 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">

370

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[TEST] Clean up all test files..."</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="371" 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">

371

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> proteinortho_cache_test_<span class="k" style="font-weight: 600;">*</span> test.<span class="k" style="font-weight: 600;">*</span> test_<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/C.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/E.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/C2.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/L.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/M.faa.<span class="k" style="font-weight: 600;">*</span><span class="o" style="font-weight: 600;">></span> /dev/null 2>&1<span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="make"></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span></span>

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> src/BUILD <span class="nb" style="color: #0086b3;">test</span>/C.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/E.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/C2.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/L.faa.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">test</span>/M.faa.<span class="k" style="font-weight: 600;">*</span></span>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> src/lapack-3.8.0/</span></pre>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Proteinortho</span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"> Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. Details can be found in <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-124"</span><span class="nt" style="color: #000080;">></span>Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124.<span class="nt" style="color: #000080;"></a></span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (<span class="idiff left right">manuscript in preparation</span>), is already build in Proteinortho. The general workflow of proteinortho is depicted <span class="p">[</span><span class="nv" style="color: #008080;">![here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.dropbox.com/s/7ubl1ginn3fmf8k/proteinortho_workflow.jpg?dl=0</span><span class="p">)</span>].</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (<span class="idiff left right">doi:10.1371/journal.pone.0105015</span>), is already build in Proteinortho. The general workflow of proteinortho is depicted <span class="p">[</span><span class="nv" style="color: #008080;">![here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.dropbox.com/s/7ubl1ginn3fmf8k/proteinortho_workflow.jpg?dl=0</span><span class="p">)</span>].</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gh" style="color: #999;"># New Features of Proteinortho Version 6!</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></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">@@ -19,7 +19,7 @@ To enhance the prediction accuracy, the relative order of genes (synteny) can be</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="gh" style="color: #999;"># Continuous Integration</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">supports</span>

</pre>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">The badge<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">The badge</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![pipeline status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/badges/master/pipeline.svg</span><span class="p">)</span>](https://gitlab.com/paulklemm_PHD/proteinortho/commits/master) indicates the current status of the continuous integration (CI) among various platforms (ubuntu, centos, debian, fedora) and GNU c++ versions (5, 6, latest)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown">The whole git repository gets deployed on a clean docker imager (gcc:latest,gcc:5,ubuntu:latest,fedora:latest,debian:latest,centos:latest) and compiled (make all) and tested (make test). The badge is green only if all test are passed. For more information see <span class="p">[</span><span class="nv" style="color: #008080;">Continuous Integration (proteinortho wiki)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Continuous%20Integration</span><span class="p">)</span>.</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="48" 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">@@ -48,17 +48,17 @@ If you cannot execute the src/BUILD/Linux_x86_64/proteinortho_clustering, then y</td>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with (bio)conda (for Linux + OSX)</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="sb" style="color: #d14;">    conda install proteinortho</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown">If you need conda (see <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.anaconda.com/anaconda/install/</span><span class="p">)</span>) and the bioconda channel: <span class="sb" style="color: #d14;">`conda config --add channels defaults && conda config --add channels bioconda && conda config --add channels conda-forge`</span>.</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/proteinortho/README.html) <span class="p">[</span><span class="nv" style="color: #008080;">![alt</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/proteinortho.svg?style=flat</span><span class="p">)</span>](https://bioconda.github.io/recipes/proteinortho/README.html)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"></span>

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with brew (for OSX)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="sb" style="color: #d14;">    brew install proteinortho</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

61

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" 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">

62

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown">If you need brew (see <span class="p">[</span><span class="nv" style="color: #008080;">here</span><span class="p">](</span><span class="sx" style="color: #d14;">https://brew.sh/index_de</span><span class="p">)</span>)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" 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">

63

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="64" 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">

64

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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with brew</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-brew-brightgreen.svg?style=flat</span><span class="p">)</span>](https://formulae.brew.sh/formula/proteinortho) <span class="p">[</span><span class="nv" style="color: #008080;">![dl</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/dynamic/json.svg?label=downloads&query=$[%27analytics%27][%27install%27][%27365d%27][%27proteinortho%27]&url=https%3A%2F%2Fformulae.brew.sh%2Fapi%2Fformula%2Fproteinortho.json&color=green</span><span class="p">)</span>](https://formulae.brew.sh/formula/proteinortho)</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="94" 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">@@ -94,8 +94,8 @@ Proteinortho uses standard software which is often installed already or is part</td>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>To <span class="nt" style="color: #000080;"><b></span>run<span class="nt" style="color: #000080;"></b></span> Proteinortho, you need: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown"><span class="p"><span class="idiff left right">  </span></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown"><span class="p"><span class="idiff left right">   </span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(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="LC97" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(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="LC98" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"><span class="p">   -</span> At least one of the following the following programs (default is diamond):</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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100

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="sb" style="color: #d14;">     - NCBI BLAST+ or NCBI BLAST legacy (to test this, type tblastn. apt-get install ncbi-blast+)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" 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">@@ -108,7 +108,7 @@ Proteinortho uses standard software which is often installed already or is part</td>

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<td class="diff-line-num old_line" data-linenumber="108" 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">

108

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="markdown"><span class="sb" style="color: #d14;">     - blat (http://hgdownload.soe.ucsc.edu/admin/)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="109" 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">

109

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<td class="diff-line-num new_line" data-linenumber="109" 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">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown"><span class="sb" style="color: #d14;">     - mmseqs2 (conda install mmseqs2, https://github.com/soedinglab/MMseqs2)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" 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">

110

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110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown"><span class="p">   -</span> Perl v5.08 or higher (to test this, type perl -v in the command line)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

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<td class="diff-line-num new_line old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown"><span class="p">   -</span> <span class="idiff left right">Python v2.6.0 or higher to include synteny analysis (to test this, type 'python -V' in the command line) </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"><span class="p">   -</span> <span class="idiff left right">(optional) Python v3.0 or higher to include synteny analysis (to test this, type 'python -V' in the command line)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="112" 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">

112

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"><span class="p">   -</span> Perl standard modules (these should come with Perl): Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with <span class="sb" style="color: #d14;">`cpan install ...`</span> )</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="113" 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">

113

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<td class="diff-line-num new_line" data-linenumber="113" 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">

113

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="nt" style="color: #000080;"></details></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" 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">

114

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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" 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">@@ -117,11 +117,11 @@ Proteinortho uses standard software which is often installed already or is part</td>

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<td class="diff-line-num old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>To <span class="nt" style="color: #000080;"><b></span>compile<span class="nt" style="color: #000080;"></b></span> Proteinortho (linux/osx), you need: (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="119" 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">

119

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"><span class="p">   -</span> GNU make (to test this, type 'make' in the command line)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

120

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<td class="diff-line-num new_line old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="markdown"><span class="p">   -</span> GNU g++ v4.1 or higher (to test this, type 'g++ --version' in the command line)<span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

121

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<td class="diff-line-num new_line old" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="markdown"><span class="p">   -</span> openmp (to test this, type 'g++ -fopenmp' in the command line)<span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(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="LC120" class="line" lang="markdown"><span class="p">   -</span> GNU g++ v4.1 or higher (to test this, type 'g++ --version' in the command line)</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(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="LC121" class="line" lang="markdown"><span class="p">   -</span> openmp (to test this, type 'g++ -fopenmp' in the command line)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="122" 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">

122

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<td class="diff-line-num new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="markdown"><span class="p">   -</span> (optional) gfortran for compiling LAPACK (to test this, type 'whereis gfortran' in the command line)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="123" 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">

123

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<td class="diff-line-num new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"><span class="p">   -</span> (optional) CMake for compiling LAPACK (to test this, type 'cmake' in the command line), OR you can use your own compiled version of lapack (you can get this with 'apt-get install liblapack3') and run 'make USEPRECOMPILEDLAPACK=TRUE'</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="markdown"><span class="idiff left right">   </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(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="LC124" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown"><span class="nt" style="color: #000080;"></details></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></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">@@ -129,23 +129,23 @@ Proteinortho uses standard software which is often installed already or is part</td>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### 2. Building and installing proteinortho from source (linux and osx)</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown">  Here you can use a working lapack library, check this with 'dpkg --get-selections | grep lapack'. Install lapack e.g. with 'apt-get install libatlas3-base' or liblapack3.</span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="markdown"><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown">  If you dont have Lapack, then 'make' will automatically compiles Lapack v3.8.0 for you !</span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="markdown">  Fetch the latest source code archive downloaded from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span><span class="idiff left right"> </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown">  Fetch the latest source code archive downloaded from <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip"</span><span class="nt" style="color: #000080;">></span>here<span class="nt" style="color: #000080;"></a></span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span> <span class="nt" style="color: #000080;"><summary></span>or from here (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="gt" style="color: #a00;">  > git clone https://gitlab.com/paulklemm_PHD/proteinortho</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="markdown"><span class="gt" style="color: #a00;"><span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"><span class="gt" style="color: #a00;">  > wget https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/master/proteinortho-master.zip</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"><span class="nt" style="color: #000080;"></details></span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="markdown"><span class="p"><span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown"><span class="p">  -</span> <span class="sb" style="color: #d14;">`tar -xzvf proteinortho*.tar.gz`</span> or <span class="sb" style="color: #d14;">`unzip proteinortho*.zip`</span> : Extract the files</span>

</pre>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"><span class="p">  -</span> <span class="sb" style="color: #d14;">`cd proteinortho*`</span> : Change directory into the extracted folder</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"><span class="p">  -</span> You can now run proteinortho6.pl directly (linux only).</span>

</pre>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown"><span class="p">  -</span> <span class="sb" style="color: #d14;">`make clean && make`</span> : If you want to recompile Proteinortho. (For osx you need a newer g++ compiler to support multithreading, see below)</span>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"><span class="p">  -</span> <span class="sb" style="color: #d14;">`make install`</span> or <span class="sb" style="color: #d14;">`make install PREFIX=~/bin`</span> if you dont have root privileges.<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"><span class="p">  -</span> <span class="sb" style="color: #d14;">`make install`</span> or <span class="sb" style="color: #d14;">`make install PREFIX=~/bin`</span> if you dont have root privileges.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown"><span class="p">  -</span> <span class="sb" style="color: #d14;">`make test`</span> : To make sure Proteinortho works as expected. The output should look like below (3. Make test output).</span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" 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">@@ -157,7 +157,7 @@ Install a newer g++ compiler for -fopenmp support (multithreading) with brew (ge</td>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown">brew install gcc --without-multilib</span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="markdown">Then you should have a g++-7 or whatever newer version that there is (g++-8,9,...).<span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(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="LC160" class="line" lang="markdown">Then you should have a g++-7 or whatever newer version that there is (g++-8,9,...).</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="markdown">Next you have to tell make to use this new compiler with one of the following:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown">ln -s /usr/local/bin/gcc-7 /usr/local/bin/gcc</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="217" 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">@@ -217,7 +217,7 @@ If you have problems compiling/running the program go to [Troubleshooting (prote</td>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="markdown"><span class="gt" style="color: #a00;">  > **proteinortho6.pl [options] \<fasta file(s)\>** (one fasta for each species, at least 2)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="markdown">  OR</span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="markdown"><span class="gt" style="color: #a00;"><span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown"><span class="gt" style="color: #a00;">  > **proteinortho [options] \<fasta file(s)\>**</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="markdown"><span class="gh" style="color: #999;"># DESCRIPTION</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">@@ -228,8 +228,7 @@ If you have problems compiling/running the program go to [Troubleshooting (prote</td>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown">  one. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr</span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="markdown">  28;12:124. To enhance the prediction accuracy, the relative order of genes</span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="markdown">  (synteny) can be used as additional feature for the discrimination of</span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="markdown">  orthologs. The corresponding extension, namely PoFF (manuscript in</span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="markdown">  preparation), is already build in Proteinortho.</span>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown">  orthologs. The corresponding extension, namely PoFF (doi:10.1371/journal.pone.0105015), is already build in Proteinortho.</span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="markdown">  Proteinortho assumes, that you have all your gene sequences in FASTA</span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown">  format either represented as amino acids or as nucleotides. The source</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">@@ -240,7 +239,7 @@ If you have problems compiling/running the program go to [Troubleshooting (prote</td>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="markdown">  -p=blastn+ (or some other algorithm). (In case you have only have NCBI</span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="markdown">  BLAST legacy installed, you need to tell this too - either by adding</span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown">  -p=blastp or -p=blastn respectively.) The full command for the example</span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="markdown">  files would thus be<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">  files would thus be</span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="markdown"><span class="gt" style="color: #a00;">  > proteinortho6.pl -project=test test/C.faa test/E.faa</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="markdown">  test/L.faa test/M.faa. Instead of naming the FASTA files one by one, you</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">@@ -253,10 +252,10 @@ If you have problems compiling/running the program go to [Troubleshooting (prote</td>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="markdown">Open <span class="sb" style="color: #d14;">`proteinorthoHelper.html`</span> in your favorite browser or visit <span class="p">[</span><span class="nv" style="color: #008080;">lechnerlab.de/proteinortho</span><span class="p">](</span><span class="sx" style="color: #d14;">http://lechnerlab.de/proteinortho/</span><span class="p">)</span> online for an interactiv exploration of the different options of proteinortho.</span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="markdown"><span class="gh" style="color: #999;"># OPTIONS<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown"><span class="gh" style="color: #999;"># OPTIONS</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Main parameters**</span> (can be used with -- or -)</span>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="markdown"><span class="p"><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="markdown"><span class="p">   -</span> <span class="gs" style="font-weight: 600;">**--project**</span>=name (default: myproject)</span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="markdown">    prefix for all resulting file names</span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="markdown"></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">@@ -290,34 +289,34 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="markdown"><span class="p"><span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="markdown"><span class="p">  -</span> <span class="gs" style="font-weight: 600;">**--p**</span>=algorithm (default: diamond)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="markdown"></span>

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<td class="diff-line-num old_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="markdown"><span class="sb" style="color: #d14;">    <details></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="markdown"><span class="sb" style="color: #d14;">      <summary>show all algorithms (Click to expand)</summary></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">      </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - blastn_legacy,blastp_legacy,tblastx_legacy : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - blastn+,blastp+,tblastx+ : standard blast family (shell commands: blastn,blastp,tblastx)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="markdown"><span class="sb" style="color: #d14;">        family. The suffix 'n' or 'p' indicates nucleotide or protein input files.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(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="LC302" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - diamond : Only for protein files! standard diamond procedure and for</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="markdown"><span class="sb" style="color: #d14;">        genes/proteins of length >40 with the additional --sensitive flag</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - lastn,lastp : lastal. -n : dna files, -p protein files (BLOSUM62</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="markdown"><span class="sb" style="color: #d14;">        scoring matrix)!</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - rapsearch : Only for protein files!<span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC309" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - rapsearch : Only for protein files!</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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">

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="markdown"></span>

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<td class="diff-line-num old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - mmseqsp,mmseqsn : mmseqs2. -n : dna files, -p protein files</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - topaz : Only for protein files!</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - usearch : usearch_local procedure with -id 0 (minimum identity</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="markdown"><span class="sb" style="color: #d14;">        percentage).</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - ublast : usearch_ublast procedure.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - blatp,blatn : blat. -n : dna files, -p protein files</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="markdown"><span class="sb" style="color: #d14;">    </details></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="markdown"><span class="sb" style="color: #d14;">    <br></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="343" 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">@@ -344,11 +343,12 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Synteny options (optional, step 2)**</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="markdown">  (This option is deprecated)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="markdown">  (output: <span class="nt" style="color: #000080;"><myproject></span>.ffadj-graph, <span class="nt" style="color: #000080;"><myproject></span>.poff.tsv (tab separated file)-graph)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="markdown"><span class="p"><span class="idiff left right">  </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC351" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="markdown"><span class="p">  -</span> <span class="gs" style="font-weight: 600;">**--synteny**</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="markdown">    activate PoFF extension to separate similar by contextual adjacencies</span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="markdown">    (requires .gff for each .fasta)</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="370" 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">@@ -370,7 +370,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC370" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="markdown"><span class="p"><span class="idiff left right">      </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="markdown"><span class="p">  -</span> <span class="gs" style="font-weight: 600;">**--singles**</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="markdown">    report singleton genes without any hit</span>

</pre>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="387" 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">@@ -387,7 +387,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="markdown">    do not generate <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>-graph file (pairwise orthology relations)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="markdown"><span class="p">  -</span> <span class="gs" style="font-weight: 600;">**--subparaCluster**</span>='options'</span>

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<td class="diff-line-num old old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="markdown">    additional parameters for the clustering algorithm (proteinortho_clustering) example -subparaCluster='-maxnodes 10000'.<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="markdown">    additional parameters for the clustering algorithm (proteinortho_clustering) example -subparaCluster='-maxnodes 10000'.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="markdown">    Note: -rmgraph cannot be set. All other parameters of subparaCluster are replacing the default values (like -cpus or -minSpecies)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="markdown"><span class="p">  -</span> <span class="gs" style="font-weight: 600;">**--xml**</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="405" 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">@@ -405,10 +405,10 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Misc options**</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC408" class="line" lang="markdown"><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>(Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="markdown"><span class="p"><span class="idiff left right">      </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="412" style="width: 35px; color: rgba(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="LC411" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="markdown"><span class="p">  -</span> <span class="gs" style="font-weight: 600;">**--cleanblast**</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="markdown">    cleans blast-graph with proteinortho_cleanupblastgraph</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="451" 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">@@ -451,7 +451,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="markdown">  copies in the presence of two very similar paralogs (default), or just to</span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="markdown">  reduce noise in the predictions by detecting multiple copies of genomic</span>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="markdown">  areas (add the parameter -dups=3). Please note that you need additional</span>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="markdown">  data to include synteny, namely the gene positions in GFF3 format.<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="markdown">  data to include synteny, namely the gene positions in GFF3 format.</span>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="markdown">  AsProteinortho is primarily made for proteins, it will only accept GFF</span>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="markdown">  entries of type CDS (column #3 in the GFF-file). The attributes column</span>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="markdown">  (#9) must contain Name=GENE IDENTIFIER where GENE IDENTIFIER corresponds</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="466" 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">@@ -466,13 +466,13 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="markdown">  test.poff.tsv (tab separated file). This file is equivalent to the test.proteinortho.tsv file (above) but</span>

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="markdown">  can be considered more accurate as synteny was involved for its</span>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="markdown">  construction.</span>

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<pre style="margin: 0;">-<span id="LC469" class="line" lang="markdown"><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="markdown"><span class="gh" style="color: #999;"># Output</span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**BLAST Search (step 1-2)**</span></span>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="markdown"><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>myproject.blast-graph (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

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<pre style="margin: 0;">-<span id="LC475" class="line" lang="markdown"><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="markdown"><span class="sb" style="color: #d14;">    filtered raw blast data based on adaptive reciprocal best blast</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="markdown"><span class="sb" style="color: #d14;">    matches (= reciprocal best match plus all reciprocal matches within a</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="markdown"><span class="sb" style="color: #d14;">    range of 95% by default) The first two rows are just comments</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="487" 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">@@ -487,7 +487,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="markdown"><span class="sb" style="color: #d14;">    evalue_ab, bitscore_ab, evalue_ba and bitscore_ba.</span></span>

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="markdown"><span class="sb" style="color: #d14;">      # file_a    file_b</span></span>

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<pre style="margin: 0;">-<span id="LC490" class="line" lang="markdown"><span class="sb" style="color: #d14;">      # a   b     evalue_ab     bitscore_ab   evalue_ba     bitscore_ba<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="markdown"><span class="sb" style="color: #d14;">      # a   b     evalue_ab     bitscore_ab   evalue_ba     bitscore_ba</span></span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="markdown"><span class="sb" style="color: #d14;">      # E.faa     C.faa   </span></span>

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="markdown"><span class="sb" style="color: #d14;">      # 3.8e-124        434.9   2.8e-126        442.2</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="markdown"><span class="sb" style="color: #d14;">      E_11  C_11  5.9e-51 190.7   5.6e-50 187.61</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="495" 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">@@ -495,7 +495,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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495

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="markdown"><span class="sb" style="color: #d14;">      ...</span></span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="markdown"> <span class="nt" style="color: #000080;"></details></span></span>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><br></span></span>

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<pre style="margin: 0;">-<span id="LC498" class="line" lang="markdown"><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="markdown"></span>

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<td class="diff-line-num old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Clustering (step 3)**</span></span>

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500

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500

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" 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">

501

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<td class="diff-line-num new_line" data-linenumber="501" 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">

501

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="542" 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">@@ -542,9 +542,9 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<td class="diff-line-num old_line" data-linenumber="542" 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">

542

</td>

<td class="diff-line-num new_line" data-linenumber="542" 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">

542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="markdown">    The html version of the myproject.proteinortho.tsv file</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="543" 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">

543

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543

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="markdown"> <span class="nt" style="color: #000080;"></details></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="544" 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">

544

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<td class="diff-line-num new_line" data-linenumber="544" 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">

544

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC544" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><br></span></span>

</pre>

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545

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<td class="diff-line-num new_line old" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC545" class="line" lang="markdown"><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="546" style="width: 35px; color: rgba(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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545

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="546" 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">

546

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546

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**POFF (-synteny)**</span></span>

</pre>

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547

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<pre style="margin: 0;">-<span id="LC547" class="line" lang="markdown"><span class="idiff left right"> </span></span>

</pre>

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547

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="548" 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">

548

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548

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="markdown">  The synteny based graph files (myproject.ffadj-graph and</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="549" 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">

549

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<td class="diff-line-num new_line" data-linenumber="549" 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">

549

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="markdown">  myproject.poff.tsv (tab separated file)-graph) have two additional columns: same_strand and</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="550" 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">

550

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<td class="diff-line-num new_line" data-linenumber="550" 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">

550

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="markdown">  simscore. The first one indicates if two genes from a match are located at</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="564" 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">@@ -564,7 +564,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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564

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564

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC564" class="line" lang="markdown"></span>

</pre>

</td>

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565

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565

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="markdown"> <span class="nt" style="color: #000080;"></details></span></span>

</pre>

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566

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566

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><br></span></span>

</pre>

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567

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<pre style="margin: 0;">-<span id="LC567" class="line" lang="markdown"><span class="idiff left right">  </span></span>

</pre>

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567

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<pre style="margin: 0;">+<span id="LC567" class="line" lang="markdown"></span>

</pre>

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568

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568

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<pre style="margin: 0;"> <span id="LC568" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><details></span></span>

</pre>

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569

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569

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<pre style="margin: 0;"> <span id="LC569" class="line" lang="markdown">  <span class="nt" style="color: #000080;"><summary></span>myproject.poff.tsv (tab separated file)-graph (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="570" 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">

570

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<td class="diff-line-num new_line" data-linenumber="570" 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">

570

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC570" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="573" 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">@@ -573,7 +573,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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573

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<td class="diff-line-num new_line" data-linenumber="573" 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">

573

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC573" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="574" 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">

574

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<td class="diff-line-num new_line" data-linenumber="574" 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">

574

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC574" class="line" lang="markdown"> <span class="nt" style="color: #000080;"></details></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="575" 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">

575

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<td class="diff-line-num new_line" data-linenumber="575" 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">

575

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><br></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

576

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<td class="diff-line-num new_line old" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC576" class="line" lang="markdown"><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

576

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC576" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="577" 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">

577

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<td class="diff-line-num new_line" data-linenumber="577" 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">

577

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC577" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="578" 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">

578

</td>

<td class="diff-line-num new_line" data-linenumber="578" 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">

578

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC578" class="line" lang="markdown"><span class="gh" style="color: #999;"># EXAMPLES</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="579" 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">

579

</td>

<td class="diff-line-num new_line" data-linenumber="579" 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">

579

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC579" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Calling proteinortho**</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="581" 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">@@ -581,14 +581,14 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="581" 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">

581

</td>

<td class="diff-line-num new_line" data-linenumber="581" 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">

581

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC581" class="line" lang="markdown">  test/</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="582" 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">

582

</td>

<td class="diff-line-num new_line" data-linenumber="582" 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">

582

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC582" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="583" 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">

583

</td>

<td class="diff-line-num new_line" data-linenumber="583" 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">

583

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC583" class="line" lang="markdown">  test/C.faa:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

584

</td>

<td class="diff-line-num new_line old" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC584" class="line" lang="markdown"><span class="gt" style="color: #a00;"><span class="idiff left right">  </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

584

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC584" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="585" 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">

585

</td>

<td class="diff-line-num new_line" data-linenumber="585" 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">

585

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC585" class="line" lang="markdown"><span class="sb" style="color: #d14;">    >C_10</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="586" 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">

586

</td>

<td class="diff-line-num new_line" data-linenumber="586" 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">

586

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC586" class="line" lang="markdown"><span class="sb" style="color: #d14;">    VVLCRYEIGGLAQVLDTQFDMYTNCHKMCSADSQVTYKEAANLTARVTTDRQKEPLTGGY</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="587" 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">

587

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<td class="diff-line-num new_line" data-linenumber="587" 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">

587

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC587" class="line" lang="markdown"><span class="sb" style="color: #d14;">    HGAKLGFLGCSLLRSRDYGYPEQNFHAKTDLFALPMGDHYCGDEGSGNAYLCDFDNQYGR</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="588" 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">

588

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<td class="diff-line-num new_line" data-linenumber="588" 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">

588

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC588" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ...</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="589" 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">

589

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<td class="diff-line-num new_line" data-linenumber="589" 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">

589

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC589" class="line" lang="markdown"></span>

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<td class="diff-line-num old_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="markdown">   test/E.faa:</span>

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<pre style="margin: 0;">-<span id="LC591" class="line" lang="markdown"><span class="gt" style="color: #a00;"><span class="idiff left right">   </span></span></span>

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<pre style="margin: 0;">+<span id="LC591" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="markdown"><span class="sb" style="color: #d14;">    >E_10</span></span>

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593

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<pre style="margin: 0;"> <span id="LC593" class="line" lang="markdown"><span class="sb" style="color: #d14;">    CVLDNYQIALLRNVLPKLFMTKNFIEGMCGGGGEENYKAMTRATAKSTTDNQNAPLSGGF</span></span>

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<pre style="margin: 0;"> <span id="LC594" class="line" lang="markdown"><span class="sb" style="color: #d14;">    NDGKMGTGCLPSAAKNYKYPENAVSGASNLYALIVGESYCGDENDDKAYLCDVNQYAPNV</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="634" 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">@@ -634,7 +634,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/</td>

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<pre style="margin: 0;"> <span id="LC634" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Example 1</span></span>

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC637" class="line" lang="markdown">In the following example a huge blast graph is used for step 3 (clustering).<span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC637" class="line" lang="markdown">In the following example a huge blast graph is used for step 3 (clustering).</span>

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="markdown">The first connected component contains 7410694 nodes, hence the kmere heuristic is activated.</span>

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="markdown">Since the fiedler vector would result in a good split, the kmere heuristic is then deactivated immediatly.</span>

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="markdown"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="657" 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">@@ -657,7 +657,7 @@ Since the fiedler vector would result in a good split, the kmere heuristic is th</td>

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="markdown"><span class="sb" style="color: #d14;">    ...</span></span>

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC659" class="line" lang="markdown"><span class="nt" style="color: #000080;"></details></span></span>

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<pre style="margin: 0;">-<span id="LC660" class="line" lang="markdown"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC661" class="line" lang="markdown"><span class="nt" style="color: #000080;"><details></span></span>

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="markdown"><span class="nt" style="color: #000080;"><summary></span>example for large graphs, where kmere is tested but not needed (Click to expand)<span class="nt" style="color: #000080;"></summary></span></span>

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="markdown"></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">@@ -692,5 +692,3 @@ Since the fiedler vector would result in a good split, the kmere heuristic is th</td>

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<pre style="margin: 0;"> <span id="LC692" class="line" lang="markdown">  Lechner, M., Findeisz, S., Steiner, L., Marz, M., Stadler, P. F., &</span>

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="markdown">  Prohaska, S. J. (2011). Proteinortho: detection of (co-) orthologs in</span>

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<pre style="margin: 0;"> <span id="LC694" class="line" lang="markdown">  large-scale analysis. BMC bioinformatics, 12(1), 124.</span></pre>

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<pre style="margin: 0;">-<span id="LC695" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC696" class="line" lang="markdown"></span></pre>

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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.<span class="idiff left right">7+dfsg-1) UNRELEASED</span>; urgency=medium</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.<span class="idiff left right">8+dfsg-1) unstable</span>; urgency=medium</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version<span class="idiff left right"> ported to Python3</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">  * debhelper-compat 12</span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">  * <span class="idiff left right">Use 2to3 to port to Python3</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * <span class="idiff left right">Fix perl interpreter path</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  <span class="idiff left right">Mon, 16 Sep 2019 12:41:53</span> +0200</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  <span class="idiff left right">Wed, 25 Sep 2019 16:39:22</span> +0200</span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">proteinortho (6.0.6+dfsg-1) unstable; urgency=medium</span>

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10

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +19,7 @@ Depends: ${shlibs:Depends},</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">         ncbi-blast+,</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">         diamond-aligner,</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">         liblapack3,</span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">         python</span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">         python<span class="idiff left right">3</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Description: Detection of (Co-)orthologs in large-scale protein analysis</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Proteinortho is a stand-alone tool that is geared towards large datasets</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> and makes use of distributed computing techniques when run on multi-core</span>

</pre>

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<li id="555c85016bd79aa8bbb523506af81b69d9c69534">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong>

deleted

</a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>

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<pre style="margin: 0;">-<span id="LC2" 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="LC3" class="line" lang="diff"><span class="p">Last-Update: Mon, 16 Sep 2019 12:41:53 +0200</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/src/proteinortho_ffadj_mcs.py</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/proteinortho_ffadj_mcs.py</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,9 +1,9 @@</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from sys import stdout, stderr, exit, argv, maxint</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from sys import stdout, stderr, exit, argv, maxsize</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> from copy import deepcopy</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> from bisect import bisect</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from itertools import izip, product</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from itertools import product</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> from os.path import basename, dirname</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> from random import randint</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> from math import ceil</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span> class Run:</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

21

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff">         adjTerm = 0</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff">         if len(self.weight) > 1:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff">             adjTerm = sum([self.weight[i] * self.weight[i+1] for i in</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                xrange(len(self.weight)-1)])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                range(len(self.weight)-1)])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">         edgeTerm = sum([w **2  for w in self.weight])</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"> #        edgeTerm = max(self.weight)**2</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">         return alpha * adjTerm + (1-alpha) * edgeTerm</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -101,9 +101,9 @@</span> def readDistsAndOrder(data, edgeThreshol</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff">         if edgeWeight < edgeThreshold:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

31

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff">             continue</span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if not g1_chromosomes.has_key(chr1):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if chr1 not in g1_chromosomes:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff">             g1_chromosomes[chr1] = set()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if not g2_chromosomes.has_key(chr2):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if chr2 not in g2_chromosomes:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff">             g2_chromosomes[chr2] = set()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

39

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff">         g1_chromosomes[chr1].add(g1)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="p">@@ -124,19 +124,19 @@</span> def readDistsAndOrder(data, edgeThreshol</span>

</pre>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff">     # add telomeres</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff">     for t1, t2 in product(tel1, tel2):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        if not res.has_key(t1):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        if t1 not in res:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff">             res[t1] = dict()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff">         res[t1][t2] = (DIRECTION_BOTH_STRANDS, 1)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#    res[maxint] = dict([</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#        (maxint, (DIRECTION_WATSON_STRAND, 1)), </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    res[maxsize] = dict([</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        (maxsize, (DIRECTION_WATSON_STRAND, 1)), </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> #        (0,      (DIRECTION_WATSON_STRAND, 1)), </span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#        (maxint, (DIRECTION_CRICK_STRAND, 1)),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        (maxsize, (DIRECTION_CRICK_STRAND, 1)),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> #        (0,      (DIRECTION_CRICK_STRAND, 1))])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#    res[maxint] = dict([</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#        (maxint, (DIRECTION_WATSON_STRAND, 1)), </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#    res[maxsize] = dict([</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        (maxsize, (DIRECTION_WATSON_STRAND, 1)), </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> #        (0,      (DIRECTION_WATSON_STRAND, 1)),</span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#        (maxint, (DIRECTION_CRICK_STRAND, 1)), </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#        (maxsize, (DIRECTION_CRICK_STRAND, 1)), </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> #        (0,      (DIRECTION_CRICK_STRAND, 1))])</span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff">     return hasMultipleChromosomes, g1, g2, res</span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="p">@@ -148,20 +148,20 @@</span> def establish_linear_genome_order(chromo</span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff">         g.append((k, -1))</span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff">         telomeres.add((k, -1))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff">         g.extend([(k, i) for i in sorted(chromosomes[k])])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g.append((k, maxint))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        telomeres.add((k, maxint))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

74

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g.append((k, maxsize))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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;">+        telomeres.add((k, maxsize))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

76

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff">     return telomeres, g</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

77

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

78

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> def insertIntoRunList(runs, runList):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    keys = map(lambda x: x.getWeight(alpha), runList)</span></span>

</pre>

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80

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    keys = [x.getWeight(alpha) for x in runList]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

81

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff">     for run in runs:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

82

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff">         i = bisect(keys, run.getWeight(alpha))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

83

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff">         keys.insert(i, run.getWeight(alpha))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

84

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff">         runList.insert(i, run)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> def checkMatching(g1, g2, g1_runs, g2_runs, runs, dist):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

87

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g1pos = dict(izip(g1, xrange(len(g1))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

88

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g2pos = dict(izip(g2, xrange(len(g2))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g1pos = dict(zip(g1, range(len(g1))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g2pos = dict(zip(g2, range(len(g2))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff">     if len(g1) != len(g2):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="p">@@ -177,7 +177,7 @@</span> def checkMatching(g1, g2, g1_runs, g2_ru</span>

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95

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff">     r_counter = 0 </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff">     prev_run = None</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff">     c_adj = 0</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for i in xrange(len(g1)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for i in range(len(g1)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff">         if not g1_runs[i]:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff">             logging.error('Gene %s is not included in any run' %g1[i])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

102

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff">             continue</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="p">@@ -213,7 +213,7 @@</span> def checkMatching(g1, g2, g1_runs, g2_ru</span>

</pre>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff">     missing_runs = all_included.symmetric_difference(runs)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff">     if missing_runs:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff">         logging.error(('Additional runs in runslist that are not part in the' + \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                ' matching: %s') %(map(str, missing_runs)))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                ' matching: %s') %(list(map(str, missing_runs))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff">     logging.info('Number of adjacencies is %s in matching of size %s.' %(c_adj,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff">         len(g1)))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="p">@@ -222,7 +222,7 @@</span> def checkMatching(g1, g2, g1_runs, g2_ru</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff">         logging.error(('Sum of run lengths does not equal matching size! Sum ' + \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff">                 'of run lengths: %s, matching size: %s') % (r_counter, len(g1)))</span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for j in xrange(len(g2)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for j in range(len(g2)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff">         if not g2_runs[j]:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff">             logging.error('Gene %s is not included in any run' %g2[j])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff">         if len(g2_runs[j]) > 1:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="p">@@ -262,8 +262,8 @@</span> def checkMatching(g1, g2, g1_runs, g2_ru</span>

</pre>

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff">                     'Weights: %s, run length: %s, run: %s') %(len(r.weight),</span>

</pre>

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff">                         g1pos[r.endG1] - g1pos[r.startG1], r)) </span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g1_chromosomes = set(map(lambda x: x[0], g1[g1pos[r.startG1]:g1pos[r.endG1]+1]))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g2_chromosomes = set(map(lambda x: x[0], g2[g2pos[r.startG2]:g2pos[r.endG2]+1]))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g1_chromosomes = set([x[0] for x in g1[g1pos[r.startG1]:g1pos[r.endG1]+1]])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g2_chromosomes = set([x[0] for x in g2[g2pos[r.startG2]:g2pos[r.endG2]+1]])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff">         if len(g1_chromosomes) != 1 and len(g2_chromosomes) != 1:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff">             logging.error(('Number of chromosomes on G1 (#chrs: %s) or G2 ' + \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff">                     '(#chrs: %s) in run %s is not 1 (Meaning that possibly' + \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="p">@@ -281,7 +281,7 @@</span> def checkMatching(g1, g2, g1_runs, g2_ru</span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff">             run_ends[r.startG1] = (r.direction, r.endG2)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff">             run_ends[r.endG1] = (r.direction, r.startG2)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for i in xrange(len(g1)-1):</span></span>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for i in range(len(g1)-1):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff">         g1i = g1[i]</span>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff">         g1i2 = g1[i+1]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff">         if g1i in run_ends and g1i2 in run_ends and run_ends[g1i][0] == \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="p">@@ -290,13 +290,13 @@</span> def checkMatching(g1, g2, g1_runs, g2_ru</span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff">             g2i = run_ends[g1i][1]</span>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff">             g2i2 = run_ends[g1i2][1]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff">             if direction == DIRECTION_CRICK_STRAND and g2pos[g2i] == g2pos[g2i2]-1:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                logging.error('Runs %s and %s could be merged, but are not!' % (map(str, g1_runs[i])[0], map(str, g1_runs[i+1])[0])) </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                logging.error('Runs %s and %s could be merged, but are not!' % (list(map(str, g1_runs[i]))[0], list(map(str, g1_runs[i+1]))[0])) </span></span>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff">             elif direction == DIRECTION_WATSON_STRAND and g2pos[g2i] == g2pos[g2i2]+1:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                logging.error('Runs %s and %s could be merged, but are not!' % (map(str, g1_runs[i])[0], map(str, g1_runs[i+1])[0]))</span></span>

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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                logging.error('Runs %s and %s could be merged, but are not!' % (list(map(str, g1_runs[i]))[0], list(map(str, g1_runs[i+1]))[0]))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff">  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"> def getAllRuns(g1, g2, d):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g2pos = dict(izip(g2, xrange(len(g2))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g2pos = dict(zip(g2, range(len(g2))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"> </span>

</pre>

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156

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff">     g1_runs = [set() for _ in g1]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

157

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff">     g2_runs = [set() for _ in g2]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

158

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="p">@@ -305,7 +305,7 @@</span> def getAllRuns(g1, g2, d):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

159

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff">     reportedRuns= list()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

160

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

161

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

162

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for i in xrange(len(g1)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

163

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for i in range(len(g1)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

164

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff">         curPos = g1[i] </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

166

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff">         </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

167

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="p">@@ -355,7 +355,7 @@</span> def getAllRuns(g1, g2, d):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

169

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff">         # if no edge exists, nothing has to be done...</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

170

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff">         if e:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            for (g2_gene, (direction, weight)) in d[curPos].items():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            for (g2_gene, (direction, weight)) in list(d[curPos].items()):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff">                 if (direction, g2_gene) not in forbiddenRunStarts:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff">                     j = g2pos[g2_gene] </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff">                     if isinstance(direction, BothStrands):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="p">@@ -391,12 +391,12 @@</span> def replaceByNew(g1_runs, g2_runs, i, j,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff">             break</span>

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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"> def doMatching(g1, g2, g1_runs, g2_runs, m, runList):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g1pos = dict(izip(g1, xrange(len(g1))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g2pos = dict(izip(g2, xrange(len(g2))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g1pos = dict(zip(g1, range(len(g1))))</span></span>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g2pos = dict(zip(g2, range(len(g2))))</span></span>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff">  </span>

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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff">     newRuns = set()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for k in xrange(g1pos[m.endG1] - g1pos[m.startG1] + 1):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for k in range(g1pos[m.endG1] - g1pos[m.startG1] + 1):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff">         i = g1pos[m.startG1] + k</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff">         j = g2pos[m.startG2] + k</span>

</pre>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"><span class="p">@@ -516,13 +516,13 @@</span> def doMatching(g1, g2, g1_runs, g2_runs,</span>

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff">     insertIntoRunList(newRuns, runList)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"> def mergeRuns(mod_g1, g1, g2, g1_runs, g2_runs, runList, alreadyMatched):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g1pos = dict(izip(g1, xrange(len(g1))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g2pos = dict(izip(g2, xrange(len(g2))))</span></span>

</pre>

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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;">+    g1pos = dict(zip(g1, range(len(g1))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g2pos = dict(zip(g2, range(len(g2))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

200

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

201

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff">     newRuns = set()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

202

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff">     wSrt = lambda x: x.getWeight(alpha)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff">     mod_g1 = list(mod_g1)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for x in xrange(len(mod_g1)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for x in range(len(mod_g1)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

206

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff">         g1i = mod_g1[x]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

207

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff">         i = g1pos[g1i]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff">         if len(g1) < i+2:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

209

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="p">@@ -601,18 +601,18 @@</span> def removeSingleGenes(genome, genome_run</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

210

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"> def findRandomRunSequence(g1, g2, dists, topXperCent):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff">     g2dists = dict()</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for g1i, x in dists.items():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for g2j, d in x.items():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

215

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for g1i, x in list(dists.items()):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

216

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for g2j, d in list(x.items()):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff">             if g2j not in g2dists:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff">                 g2dists[g2j] = dict()</span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff">             g2dists[g2j][g1i] = d</span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff">     # copy g1, g2 and dists map, because we'll modify it. Also remove all genes</span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff">     # that do not contain edges.</span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g1 = [x for x in g1 if dists.has_key(x) and len(dists[x])]</span></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g2 = [x for x in g2 if g2dists.has_key(x) and len(g2dists[x])]</span></span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g1 = [x for x in g1 if x in dists and len(dists[x])]</span></span>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g2 = [x for x in g2 if x in g2dists and len(g2dists[x])]</span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff"> </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;">-    g1pos = dict(izip(g1, xrange(len(g1))))</span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g1pos = dict(zip(g1, range(len(g1))))</span></span>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff">     g1_runs, g2_runs, runs = getAllRuns(g1, g2, dists)</span>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="diff">     logging.info('Found %s runs.' %len(runs))</span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff"><span class="p">@@ -621,7 +621,7 @@</span> def findRandomRunSequence(g1, g2, dists,</span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff">     </span>

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<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff">     res = set()</span>

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff">     while runList:</span>

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<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        noOfAdjacencies = len(filter(lambda x: x.getWeight(alpha) and x.getWeight(alpha) or 0, runList))</span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        noOfAdjacencies = len([x for x in runList if x.getWeight(alpha) and x.getWeight(alpha) or 0])</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff">         if noOfAdjacencies:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="diff">             randPos = randint(1, ceil(noOfAdjacencies * topXperCent))</span>

</pre>

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff">         else:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"><span class="p">@@ -645,7 +645,7 @@</span> def findRandomRunSequence(g1, g2, dists,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff">                 for g in del_g1.intersection(mod_g1):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff">                     mod_g1.remove(g)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                g1pos = dict(izip(g1, xrange(len(g1))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                g1pos = dict(zip(g1, range(len(g1))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff">             # add new modification points</span>

</pre>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="diff">             mod_g1.update(new_mod_g1)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC250" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="diff"><span class="p">@@ -653,7 +653,7 @@</span> def findRandomRunSequence(g1, g2, dists,</span>

</pre>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff">             if del_g2:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC253" class="line" lang="diff">                 logging.info('Zombie genes removed from G2: %s' %', '.join(map(str, del_g2)))</span>

</pre>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="diff">                 for g2j in mod_g2:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    for g1i, (d, _) in g2dists[g2j].items():</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                    for g1i, (d, _) in list(g2dists[g2j].items()):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff">                         if g1i in g1:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff">                             if d == DIRECTION_CRICK_STRAND:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff">                                 mod_g1.add(g1i)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"><span class="p">@@ -665,8 +665,8 @@</span> def findRandomRunSequence(g1, g2, dists,</span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff">                     runList, res)</span>

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff">   </span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="diff">     if res: </span>

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<pre style="margin: 0;">-<span id="LC264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        logging.info('Matching finished. Longest run size is %s.' %(max(map(len,</span></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            res))))</span></span>

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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        logging.info('Matching finished. Longest run size is %s.' %(max(list(map(len,</span></span>

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<pre style="margin: 0;">-<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            res)))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="diff">     else:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff">         logging.info('Matching finished, but no runs found. Empty input?')</span>

</pre>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"><span class="p">@@ -681,19 +681,19 @@</span> def repeatMatching(g1, g2, g1_mod, g2_mo</span>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff">     g2_runs_res = g2_runs</span>

</pre>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff">     selectedRuns_res = list()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g1pos = dict(izip(g1_mod, xrange(len(g1_mod))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g2pos = dict(izip(g2_mod, xrange(len(g2_mod))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g1pos = dict(zip(g1_mod, range(len(g1_mod))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g2pos = dict(zip(g2_mod, range(len(g2_mod))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC280" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff">     noReps = repMatching</span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff">     while repMatching:</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;">-        for i in xrange(len(g1_runs)):</span></span>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for i in range(len(g1_runs)):</span></span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff">             run_set = g1_runs[i]</span>

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff">             if len(run_set) != 1:</span>

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<pre style="margin: 0;">-<span id="LC288" class="line" lang="diff">                 logging.error(('Expected run, set length of 1, but was told' + \</span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff">                         ' different: %s.') %(', '.join(map(str, run_set))))</span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            run = run_set.__iter__().next() </span></span>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            run = next(run_set.__iter__()) </span></span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff">             g1i = g1_mod[i]</span>

</pre>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff"><span class="p">@@ -720,11 +720,11 @@</span> def repeatMatching(g1, g2, g1_mod, g2_mo</span>

</pre>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff">                     len(g1_mod), noReps-repMatching+2))</span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff">         # remove runs that fall below min length of minCsSize</span>

</pre>

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        ff = lambda x: len(x.__iter__().next()) >= minCsSize</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g1_mod = [g1_mod[i] for i in xrange(len(g1_mod)) if ff(g1_runs[i])]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g2_mod = [g2_mod[i] for i in xrange(len(g2_mod)) if ff(g2_runs[i])]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g1_runs = filter(ff, g1_runs)</span></span>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g2_runs = filter(ff, g2_runs)</span></span>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        ff = lambda x: len(next(x.__iter__())) >= minCsSize</span></span>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g1_mod = [g1_mod[i] for i in range(len(g1_mod)) if ff(g1_runs[i])]</span></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g2_mod = [g2_mod[i] for i in range(len(g2_mod)) if ff(g2_runs[i])]</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g1_runs = list(filter(ff, g1_runs))</span></span>

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g2_runs = list(filter(ff, g2_runs))</span></span>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="diff">         selectedRuns = set([s for s in selectedRuns if len(s) >= minCsSize])</span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="diff">         # stop if no runs were found matching the criteria</span>

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<pre style="margin: 0;">-<span id="LC312" class="line" lang="diff"><span class="p">@@ -736,10 +736,10 @@</span> def repeatMatching(g1, g2, g1_mod, g2_mo</span>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff">         logging.info('%s feasible runs retained.' %len(selectedRuns))</span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff">         # reconciliate with result data</span>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g2pos = dict(izip(g2_mod, xrange(len(g2_mod))))</span></span>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g1pos = dict(izip(g1_mod, xrange(len(g1_mod))))</span></span>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g2pos_res = dict(izip(g2_mod_res, xrange(len(g2_mod_res))))</span></span>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        g1pos_res = dict(izip(g1_mod_res, xrange(len(g1_mod_res))))</span></span>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g2pos = dict(zip(g2_mod, range(len(g2_mod))))</span></span>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g1pos = dict(zip(g1_mod, range(len(g1_mod))))</span></span>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g2pos_res = dict(zip(g2_mod_res, range(len(g2_mod_res))))</span></span>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        g1pos_res = dict(zip(g1_mod_res, range(len(g1_mod_res))))</span></span>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff">         </span>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff">         chr_srt = lambda x, y: x[0] == y[0] and (x[1] < y[1] and -1 or 1) or (x[0] < y[0] and -1 or 1)</span>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff">         g1_mod_new = sorted(set(g1_mod_res + g1_mod), cmp=chr_srt)</span>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="diff"><span class="p">@@ -749,17 +749,17 @@</span> def repeatMatching(g1, g2, g1_mod, g2_mo</span>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="diff">         for g1i in g1_mod_new:</span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff">             x = set()</span>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if g1pos_res.has_key(g1i):</span></span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if g1i in g1pos_res:</span></span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff">                 x.update(g1_runs_res[g1pos_res[g1i]])</span>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if g1pos.has_key(g1i):</span></span>

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if g1i in g1pos:</span></span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff">                 x.update(g1_runs[g1pos[g1i]])</span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff">             g1_runs_new.append(x)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff">         for g2j in g2_mod_new:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="diff">             x = set()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if g2pos_res.has_key(g2j):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if g2j in g2pos_res:</span></span>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="diff">                 x.update(g2_runs_res[g2pos_res[g2j]])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if g2pos.has_key(g2j):</span></span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if g2j in g2pos:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff">                 x.update(g2_runs[g2pos[g2j]])</span>

</pre>

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<pre style="margin: 0;">-<span id="LC347" class="line" lang="diff">             g2_runs_new.append(x) </span>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="diff"><span class="p">@@ -776,21 +776,21 @@</span> def repeatMatching(g1, g2, g1_mod, g2_mo</span>

</pre>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"> def printMatching(g1, g2, g1_runs, hasMultipleChromosomes, out):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="diff">     if hasMultipleChromosomes:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print >> f, 'Chr(G1)\tG1\tChr(G2)\tG2\tdirection\tedge weight'</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print('Chr(G1)\tG1\tChr(G2)\tG2\tdirection\tedge weight', file=f)</span></span>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="diff">     else:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print >> f, 'G1\tG2\tdirection\tedge weight'</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print('G1\tG2\tdirection\tedge weight', file=f)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g2pos = dict(izip(g2, xrange(len(g2))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    g1pos = dict(izip(g1, xrange(len(g1))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g2pos = dict(zip(g2, range(len(g2))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    g1pos = dict(zip(g1, range(len(g1))))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="diff"> </span>

</pre>

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365

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<pre style="margin: 0;">-<span id="LC365" class="line" lang="diff">     cur_index = dict()</span>

</pre>

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366

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for i in xrange(len(g1_runs)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

367

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for i in range(len(g1_runs)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

368

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<pre style="margin: 0;">-<span id="LC368" class="line" lang="diff">         run_set = g1_runs[i]</span>

</pre>

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369

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<pre style="margin: 0;">-<span id="LC369" class="line" lang="diff">         for run in run_set:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC370" class="line" lang="diff">             g1i = g1[i]</span>

</pre>

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="diff">             j = 0</span>

</pre>

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<pre style="margin: 0;">-<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if cur_index.has_key(run):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if run in cur_index:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="diff">                 j = cur_index[run]</span>

</pre>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="diff">             if run.direction == DIRECTION_CRICK_STRAND:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="diff">                 g2j = g2[g2pos[run.startG2] + j]</span>

</pre>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="diff"><span class="p">@@ -800,22 +800,22 @@</span> def printMatching(g1, g2, g1_runs, hasMu</span>

</pre>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="diff">             direction = run.direction == DIRECTION_CRICK_STRAND and '1' or '-1'</span>

</pre>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="diff">             g1i1 = g1i[1] == -1 and 'TELOMERE_START' or g1i[1]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            g1i1 = g1i[1] == maxint and 'TELOMERE_END' or g1i1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            g1i1 = g1i[1] == maxsize and 'TELOMERE_END' or g1i1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="diff">             g2j1 = g2j[1] == -1 and 'TELOMERE_START' or g2j[1]</span>

</pre>

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384

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC384" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            g2j1 = g2j[1] == maxint and 'TELOMERE_END' or g2j1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

385

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC385" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            g2j1 = g2j[1] == maxsize and 'TELOMERE_END' or g2j1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

386

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC386" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

387

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC387" class="line" lang="diff">             if hasMultipleChromosomes:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

388

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                print >> f, '%s\t%s\t%s\t%s\t%s\t%s' %(g1i[0], g1i1, g2j[0],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

389

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC389" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        g2j1, direction, run.weight[j])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

390

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC390" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                print('%s\t%s\t%s\t%s\t%s\t%s' %(g1i[0], g1i1, g2j[0],</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

391

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        g2j1, direction, run.weight[j]), file=f)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

392

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC392" class="line" lang="diff">             else:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

393

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC393" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                print >> f, '%s\t%s\t%s\t%s' %(g1i1, g2j1, direction,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

394

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        run.weight[j])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

395

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                print('%s\t%s\t%s\t%s' %(g1i1, g2j1, direction,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

396

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC396" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        run.weight[j]), file=f)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

397

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC397" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

398

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC398" class="line" lang="diff">             cur_index[run] = j+1</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

399

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

400

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC400" class="line" lang="diff"> if __name__ == '__main__':</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

401

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC401" class="line" lang="diff">     if len(argv) < 3 or len(argv) > 8:</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

402

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print '\tusage: %s <DIST FILE> <ALPHA> [ <EDGE WEIGHT THRESHOLD> --repeat-matching (-R) <NUMBER >= 2> --min-cs-size (-M) <NUMBER >= 1> ]' %argv[0]</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

403

</td>

<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print('\tusage: %s <DIST FILE> <ALPHA> [ <EDGE WEIGHT THRESHOLD> --repeat-matching (-R) <NUMBER >= 2> --min-cs-size (-M) <NUMBER >= 1> ]' %argv[0])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

404

</td>

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="diff">         exit(1)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

405

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<pre style="margin: 0;">-<span id="LC405" class="line" lang="diff">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="diff">     repMatching= '--repeat-matching' in argv or '-R' in argv</span>

</pre>

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407

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<pre style="margin: 0;">-<span id="LC407" class="line" lang="diff"><span class="p">@@ -826,8 +826,8 @@</span> if __name__ == '__main__':</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

408

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<pre style="margin: 0;">-<span id="LC408" class="line" lang="diff">         minCsSize = int(argv[pos+1])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC409" class="line" lang="diff">         argv = argv[:pos] + argv[pos+2:]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

410

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<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff">         if not repMatching:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

411

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            print >> stderr, ('Argument --min-cs-size (-M) only valid in ' + \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    'combination with --repeat-matching (-R)')</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            print(('Argument --min-cs-size (-M) only valid in ' + \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                    'combination with --repeat-matching (-R)'), file=stderr)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

415

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="diff">             exit(1)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

416

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="diff">     else:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

417

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="diff">         minCsSize = 1</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

418

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="diff"><span class="p">@@ -869,7 +869,7 @@</span> if __name__ == '__main__':</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="diff">     # sum of weights of adjacencies</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

420

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="diff">     wAdj = sum([r.getWeight(1) for r in selectedRuns])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="diff">     # sum of weights of all edges of the matching</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    wEdg = sum([sum(map(lambda x: x**2, r.weight)) for r in selectedRuns])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    wEdg = sum([sum([x**2 for x in r.weight]) for r in selectedRuns])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

425

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<pre style="margin: 0;">-<span id="LC425" class="line" lang="diff">     edg = sum(map(len, selectedRuns))</span>

</pre>

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426

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<pre style="margin: 0;">-<span id="LC426" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

427

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="diff"><span class="p">@@ -892,6 +892,6 @@</span> if __name__ == '__main__':</span>

</pre>

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428

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff">             ' is %s with #edg = %s, adj(M) = %.3f and edg(M) = %.3f') %(bkp, edg,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

429

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<pre style="margin: 0;">-<span id="LC429" class="line" lang="diff">                 wAdj, wEdg))</span>

</pre>

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430

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

431

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print '#bkp\t#edg\tadj\tedg'</span></span>

</pre>

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432

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<pre style="margin: 0;">-<span id="LC432" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print '%s\t%s\t%.6f\t%.6f' %(bkp, edg, wAdj, wEdg)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

433

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<pre style="margin: 0;">-<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print('#bkp\t#edg\tadj\tedg')</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

434

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print('%s\t%s\t%.6f\t%.6f' %(bkp, edg, wAdj, wEdg))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

435

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>

deleted

</a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2to3.patch</span></pre>

</td>

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</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,3 +15,9 @@ override_dh_auto_install:</td>

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15

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15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_fixperms:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

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16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">     dh_fixperms</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">     find debian \( -name "*.faa" -o -name "*.gff" \) -exec chmod -x \{\} \;</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">override_dh_install:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">     dh_install</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">     for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="plaintext">         sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="plaintext">     done</span></pre>

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<br>

</li>

<li id="c9e37a96ac72f9ef076d7a41a57470524d63b36e">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#c9e37a96ac72f9ef076d7a41a57470524d63b36e"><strong>proteinortho6.pl</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,7 +3,7 @@</td>

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3

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<td class="diff-line-num new_line" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   This file is part of Proteinortho.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num 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">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   (C) 2009/2010 Marcus Lechner</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="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">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   Proteinortho is free software; you can redistribute it and/or modify</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   it under the terms of the GNU General Public License as published</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   by the Free Software Foundation; either version 2, or (at your</span></span>

</pre>

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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>

<td class="diff-line-num unfold js-unfold new_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>

<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 +17,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   You should have received a copy of the GNU General Public License</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line" data-linenumber="18" 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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   along with Proteinortho; see the file COPYING.  If not, write to the</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   Free Software Foundation, Inc., 59 Temple Place - Suite 330,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   Boston, MA 02111-1307, USA.<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#   Boston, MA 02111-1307, USA.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

23

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># About</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Proteinortho</span></span>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># input fasta files with proteins</span></span>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># output matrix with orthologous proteins</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @authors Marcus Lechner, Clemens Elias Thoelken, Paul Klemm</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @email lechner\@staff.uni-marburg.de</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @company University of Maruburg</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"></span>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##MARK_FOR_NEW_BLAST_ALGORITHM => FLAG for adding a new blast algorithm.<span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(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="LC36" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##MARK_FOR_NEW_BLAST_ALGORITHM => FLAG for adding a new blast algorithm.</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">### ============================================================================</span></span>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">### MAN-PAGE</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="215" 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">@@ -215,7 +215,7 @@ do not generate .graph file (pairwise orthology relations)</td>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item B<--subparaCluster>='options'</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="perl"></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">additional parameters for the clustering algorithm (proteinortho_clustering) example -subparaCluster='-maxnodes 10000'.<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">additional parameters for the clustering algorithm (proteinortho_clustering) example -subparaCluster='-maxnodes 10000'.</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Note: -rmgraph cannot be set. All other parameters of subparaCluster are replacing the default values (like -cpus or -minSpecies)</span></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item B<--xml></span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="268" 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">@@ -268,7 +268,7 @@ If you want to involve multiple machines or separate a Proteinortho run into sma</td>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">First, run 'proteinortho6.pl -steps=1 ...' to generate the indices.</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Then you can run 'proteinortho6.pl -steps=2 -jobs=B<M>/B<N> ...' to run small chunks separately.</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Instead of B<M> and B<N> numbers must be set representing the number of jobs you want to divide the run into (B<M>) and the job division to be performed by the process.</span></span>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">E.g. to divide a Proteinortho run into 4 jobs to run on several machines, use<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">E.g. to divide a Proteinortho run into 4 jobs to run on several machines, use</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=back</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="278" 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">@@ -278,7 +278,7 @@ E.g. to divide a Proteinortho run into 4 jobs to run on several machines, use</td>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=over 4</span></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="perl"></span>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B<blast-graph><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B<blast-graph></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">filtered raw blast data based on adaptive reciprocal best blast</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">matches (= reciprocal best match plus all reciprocal matches within a</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="289" 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">@@ -289,12 +289,12 @@ about to follow. E.g. # M.faa L.faa tells that the next lines representing</td>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">results for species M and L. All matches are reciprocal matches. If</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">e.g. a match for M_15 L_15 is shown, L_15 M_15 exists implicitly.</span></span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">E-Values and bit scores for both directions are given behind each</span></span>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">match. The 4 comment numbers ('# 3.8e-124        434.9...') are representing the median values of<span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC292" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">match. The 4 comment numbers ('# 3.8e-124        434.9...') are representing the median values of</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">evalue_ab, bitscore_ab, evalue_ba and bitscore_ba.</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  ----------------------------------------</span></span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  # file_a  file_b<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  # a b evalue_ab bitscore_ab evalue_ba bitscore_ba<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  # file_a  file_b</span></span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  # a b evalue_ab bitscore_ab evalue_ba bitscore_ba</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  # E.faa C.faa</span></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  # 3.8e-124        434.9   2.8e-126        442.2</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  E_10  C_10  3.8e-124  434.9 2.8e-126  442.2</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="307" 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">@@ -307,7 +307,7 @@ evalue_ab, bitscore_ab, evalue_ba and bitscore_ba.</td>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=over 4</span></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B<proteinortho-graph><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B<proteinortho-graph></span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">clustered myproject.blast-graph. Its connected components are represented in myproject.proteinortho.tsv. The format is the same as the blast-graph (see above).</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="319" 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">@@ -319,7 +319,7 @@ clustered myproject.blast-graph. Its connected components are represented in myp</td>

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  E_11  C_11  5.9e-51 190.7 5.6e-50 187.6</span></span>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">  ----------------------------------------</span></span>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="perl"></span>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B<proteinortho><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B<proteinortho></span></span>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The connected components.</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The first line starting with #is a comment line indicating the meaning of each column for each of the following lines which represent an orthologous group each.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="341" 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">@@ -341,6 +341,8 @@ By default, Proteinortho splits each group into two more dense subgroups when th</td>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head2 POFF (-synteny)</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="perl"></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">-->> This option is deprecated <<---</span></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The synteny based graph files (myproject.ffadj-graph and myproject.poff-graph) have two additional columns:</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">same_strand and simscore. The first one indicates if two genes from a match are located at the same strands (1) or not (-1).</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The second one is an internal score which can be interpreted as a normalized weight ranging from 0 to 1 based on the respective e-values.</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">@@ -355,7 +357,7 @@ Moreover, a second comment line is followed after the species lines, e.g.</td>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B>ffadj-graph></span></span>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="perl"></span>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">filtered blast data based on adaptive reciprocal best blast matches and synteny (only if -synteny is set)<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC360" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">filtered blast data based on adaptive reciprocal best blast matches and synteny (only if -synteny is set)</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=item <myproject>.B<poff-graph></span></span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="perl"></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">@@ -404,7 +406,7 @@ To do so, add the parameter -synteny.</td>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">You can use it to either come closer to one-to-one orthology relations by preferring synthetically conserved copies in the presence of two very similar paralogs (default),</span></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">or just to reduce noise in the predictions by detecting multiple copies of genomic areas (add the parameter -dups=3).</span></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Please note that you need additional data to include synteny, namely the gene positions in GFF3 format.</span></span>

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<pre style="margin: 0;">-<span id="LC407" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">As Proteinortho is primarily made for proteins, it will only accept GFF entries of type CDS (column #3 in the GFF-file).<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">As Proteinortho is primarily made for proteins, it will only accept GFF entries of type CDS (column #3 in the GFF-file).</span></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The attributes column (#9) must contain Name=GENE IDENTIFIER where GENE IDENTIFIER corresponds to the respective identifier in the FASTA format.</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">It may not contain a semicolon (;)! Alternatively, you can also set ID=GENE IDENTIFIER.</span></span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Example files are provided in the source code archive.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="427" 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">@@ -425,7 +427,7 @@ The directory src contains useful tools, e.g. proteinortho_grab_proteins.pl whic</td>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head1 AUTHORS</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="perl"></span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Marcus Lechner (lechner\@staff.uni-marburg.de), Clemens Elias Thoelken, Paul Klemm<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Marcus Lechner (lechner\@staff.uni-marburg.de), Clemens Elias Thoelken, Paul Klemm</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head1 ONLINE INFORMATION</span></span>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="455" 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">@@ -453,7 +455,7 @@ use POSIX;</td>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<td class="diff-line-num new_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>

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<td class="diff-line-num new_line" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<pre style="margin: 0;">-<span id="LC456" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.<span class="idiff left right">6</span></span><span class="p">";</span></span>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">6.0.<span class="idiff left right">8</span></span><span class="p">";</span></span>

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<td class="diff-line-num new_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>

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<td class="diff-line-num new_line" data-linenumber="460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / be verbose</span></span>

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<td class="diff-line-num new_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span>   <span class="c1" style="color: #998; font-style: italic;"># 0/1   -> don't / show debug data</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="507" 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">@@ -505,7 +507,7 @@ our $all_jobs_submitted :shared = 0;</td>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$po_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

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<td class="diff-line-num old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$run_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="509" 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">

509

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">gene_counter</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># Holds the number of genes for each data file (for sorting)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC508" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">max_gene_length_diamond</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># Holds the maximum length of genes for each data file (for diamond -> -sensitive option)<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC510" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">max_gene_length_diamond</span><span class="p">;</span>    <span class="c1" style="color: #998; font-style: italic;"># Holds the maximum length of genes for each data file (for diamond -> -sensitive option)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="509" 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">

509

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<td class="diff-line-num new_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$threads_per_process</span> <span class="p">:</span><span class="nv" style="color: #008080;">shared</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Number of subthreads for blast</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="510" 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">

510

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<td class="diff-line-num new_line" data-linenumber="512" 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">

512

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$freemem_inMB</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># -1 = detect automatically with 'free -m'</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="530" 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">@@ -528,7 +530,7 @@ our $NC="\033[0m"; # No Color</td>

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530

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$tput</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">tput color 2>/dev/null</span><span class="p">`;</span> <span class="c1" style="color: #998; font-style: italic;"># test if the shell supports colors</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="532" 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">

532

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="perl"><span class="nv" style="color: #008080;">$tput</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC531" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tput</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/[^0-9]|^&/</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tput</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="533" style="width: 35px; color: rgba(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="LC533" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tput</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">m/[^0-9]|^&/</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tput</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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532

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<td class="diff-line-num new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="perl">  <span class="nv" style="color: #008080;">$RED</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="perl">  <span class="nv" style="color: #008080;">$GREEN</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>

</pre>

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536

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="perl">  <span class="nv" style="color: #008080;">$ORANGE</span><span class="o" style="font-weight: 600;">=</span><span class="p">"";</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="555" 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">@@ -553,11 +555,11 @@ foreach my $option (@ARGV) {</td>

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<td class="diff-line-num old_line" data-linenumber="553" 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">

553

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<td class="diff-line-num new_line" data-linenumber="555" 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">

555

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cleanblast$/</span><span class="p">)</span>       <span class="p">{</span> <span class="nv" style="color: #008080;">$checkblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span>  <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="554" 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">

554

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<td class="diff-line-num new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cleanupblast$/</span><span class="p">)</span>       <span class="p">{</span> <span class="nv" style="color: #008080;">$checkblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span>  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="555" 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">

555

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<td class="diff-line-num new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?verbose=(0|1)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span>  <span class="p">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

556

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<td class="diff-line-num new_line old" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC556" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?te?mp=(.+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new old_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

558

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?te?mp=(.+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="557" 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">

557

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<td class="diff-line-num new_line" data-linenumber="559" 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">

559

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="perl">                <span class="c1" style="color: #998; font-style: italic;"># make sure it ends with /</span></span>

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<td class="diff-line-num old_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="perl">                <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\/$/</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">/</span><span class="p">";}</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$pwd</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$ENV</span><span class="p">{"</span><span class="s2" style="color: #d14;">HOME</span><span class="p">"};</span> <span class="nv" style="color: #008080;">$tmp_path</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/~/$pwd/g</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="perl">                <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">d</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">R</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">W</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="p">){</span></span>

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560

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<td class="diff-line-num new_line old" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC560" class="line" lang="perl">                  <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;"> -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> is not accessible. Check if the directory exists and is read- and writable.</span><span class="p">");</span><span class="idiff left right">  </span></span>

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<td class="diff-line-num new new_line" data-linenumber="562" style="width: 35px; color: rgba(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="LC562" class="line" lang="perl">                  <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;"> -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> is not accessible. Check if the directory exists and is read- and writable.</span><span class="p">");</span></span>

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561

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<td class="diff-line-num new_line" data-linenumber="563" 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">

563

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="perl">                <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

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562

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<td class="diff-line-num new_line" data-linenumber="564" 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">

564

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="perl">                  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/proteinortho_cache/</span><span class="p">){</span></span>

</pre>

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563

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<td class="diff-line-num new_line" data-linenumber="565" 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">

565

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="perl">                    <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="575" 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">@@ -573,8 +575,8 @@ foreach my $option (@ARGV) {</td>

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573

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<td class="diff-line-num new_line" data-linenumber="575" 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">

575

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cpus=auto$/</span><span class="p">)</span>          <span class="p">{</span> <span class="nv" style="color: #008080;">$cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="574" 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">

574

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<td class="diff-line-num new_line" data-linenumber="576" 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">

576

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<pre style="margin: 0;"> <span id="LC576" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?alpha=([0-9\.]+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$alpha</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="575" 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">

575

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<td class="diff-line-num new_line" data-linenumber="577" 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">

577

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<pre style="margin: 0;"> <span id="LC577" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?purity=([0-9\.]+)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$purity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

576

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<td class="diff-line-num new_line old" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC576" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?report=([0-9]+)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$report</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

577

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<td class="diff-line-num new_line old" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC577" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?minspecies=([0-9.]+)$/</span><span class="p">)</span>       <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$minspecies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">the argument -minspecies=$1 is invalid.</span><span class="si" style="color: #d14;">$RED</span><span class="s2" style="color: #d14;"> minspecies needs to be >=0!</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">minspecies: the min. number of genes per species. If a group is found with up to (minspecies) genes/species, it wont be split again (regardless of the connectivity).</span><span class="p">");}</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

578

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<pre style="margin: 0;">+<span id="LC578" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?report=([0-9]+)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$report</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

579

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC579" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?minspecies=([0-9.]+)$/</span><span class="p">)</span>       <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span><span class="nv" style="color: #008080;">$minspecies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">the argument -minspecies=$1 is invalid.</span><span class="si" style="color: #d14;">$RED</span><span class="s2" style="color: #d14;"> minspecies needs to be >=0!</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">minspecies: the min. number of genes per species. If a group is found with up to (minspecies) genes/species, it wont be split again (regardless of the connectivity).</span><span class="p">");}</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="578" 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">

578

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<td class="diff-line-num new_line" data-linenumber="580" 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">

580

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<pre style="margin: 0;"> <span id="LC580" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?conn=([0-9\.]+)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$connectivity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="579" 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">

579

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<td class="diff-line-num new_line" data-linenumber="581" 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">

581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cov=([0-9]+)$/</span><span class="p">)</span>       <span class="p">{</span> <span class="nv" style="color: #008080;">$coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="580" 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">

580

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<td class="diff-line-num new_line" data-linenumber="582" 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">

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?mcl$/</span><span class="p">)</span>        <span class="p">{</span> <span class="nv" style="color: #008080;">$useMcl</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="590" 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">@@ -588,36 +590,36 @@ foreach my $option (@ARGV) {</td>

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<td class="diff-line-num old_line" data-linenumber="588" 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">

588

</td>

<td class="diff-line-num new_line" data-linenumber="590" 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">

590

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<pre style="margin: 0;"> <span id="LC590" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?sim=([0-9\.]+)$/</span><span class="p">)</span>       <span class="p">{</span> <span class="nv" style="color: #008080;">$sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="589" 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">

589

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<td class="diff-line-num new_line" data-linenumber="591" 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">

591

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC591" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?startat=([0-9]+)$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$startat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="590" 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">

590

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<td class="diff-line-num new_line" data-linenumber="592" 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">

592

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?stopat=([0-9]+)$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$stopat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

591

</td>

<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC591" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?jobs?=([\d]+)\/([\d]+)$/</span><span class="p">)</span>   <span class="p">{</span> <span class="nv" style="color: #008080;">$jobnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="nv" style="color: #008080;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$2</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

592

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<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC592" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?selfblast$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

593

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<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC593" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?selfblast=(0|1)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

594

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<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC594" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?singles$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$singles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

595

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<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC595" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?singles=(0|1)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$singles</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

596

</td>

<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC596" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?poff$/</span><span class="p">)</span>       <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p"><span class="idiff left">}</span></span><span class="idiff right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

597

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<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC597" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p"><span class="idiff left">}</span></span><span class="idiff right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

598

</td>

<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC598" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny=(0|1)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

599

</td>

<td class="diff-line-num new_line old" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC599" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?dups=0$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$duplication</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

593

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC593" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?jobs?=([\d]+)\/([\d]+)$/</span><span class="p">)</span>   <span class="p">{</span> <span class="nv" style="color: #008080;">$jobnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="nv" style="color: #008080;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$2</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

594

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC594" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?selfblast$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

595

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC595" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?selfblast=(0|1)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

596

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<pre style="margin: 0;">+<span id="LC596" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?singles$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$singles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

597

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC597" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?singles=(0|1)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$singles</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC598" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?poff$/</span><span class="p">)</span>       <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">[WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -->> This option is deprecated <<---</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

599

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC599" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">[WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -->> This option is deprecated <<---</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

600

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC600" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?synteny=(0|1)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">[WARNING]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -->> This option is deprecated <<---</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff right"> </span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

601

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC601" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?dups=0$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$duplication</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="600" 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">

600

</td>

<td class="diff-line-num new_line" data-linenumber="602" 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">

602

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC602" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?dups=([1-8])$/</span><span class="p">)</span>   <span class="p">{</span> <span class="nv" style="color: #008080;">$duplication</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

601

</td>

<td class="diff-line-num new_line old" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC601" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?neighbourjoin$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$neighbourjoin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

603

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC603" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?neighbourjoin$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$neighbourjoin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="602" 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">

602

</td>

<td class="diff-line-num new_line" data-linenumber="604" 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">

604

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC604" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?neighbourjoin=(0|1)$/</span><span class="p">)</span>  <span class="p">{</span> <span class="nv" style="color: #008080;">$neighbourjoin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

603

</td>

<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC603" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cs=([0-9]+)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$cs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

604

</td>

<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC604" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?keep$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

605

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC605" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?force$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

606

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC606" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?clean$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

607

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC607" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?help$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

608

</td>

<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC608" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?test$/</span><span class="p">)</span>     <span class="p">{</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">check_bins</span><span class="p">;</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">get_po_path</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">All necessary proteinortho_* binaries are found.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

609

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC609" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?h$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

610

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC610" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?nograph$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

611

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC611" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?xml$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$doxml</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

612

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC612" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?graph$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

613

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC613" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?desc$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span><span class="idiff left right">  </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

605

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC605" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cs=([0-9]+)$/</span><span class="p">)</span>    <span class="p">{</span> <span class="nv" style="color: #008080;">$cs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC606" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?keep$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC607" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?force$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

608

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC608" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?clean$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$clean</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

609

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC609" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?help$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

610

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC610" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?test$/</span><span class="p">)</span>     <span class="p">{</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">check_bins</span><span class="p">;</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">get_po_path</span><span class="p">;</span> <span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">All necessary proteinortho_* binaries are found.</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?h$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

612

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC612" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?nograph$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

613

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC613" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?xml$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$doxml</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

614

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC614" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?graph$/</span><span class="p">)</span>      <span class="p">{</span> <span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

615

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC615" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?desc$/</span><span class="p">)</span>     <span class="p">{</span> <span class="nv" style="color: #008080;">$desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="614" 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">

614

</td>

<td class="diff-line-num new_line" data-linenumber="616" 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">

616

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC616" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?project=(.*)$/</span><span class="p">)</span>   <span class="p">{</span> <span class="nv" style="color: #008080;">$project</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;</span> <span class="nv" style="color: #008080;">$project</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\/* \t\:\~\&\%\$\§\"\(\)\[\]\{\}\^\\]//g</span><span class="p">;</span> <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="615" 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">

615

</td>

<td class="diff-line-num new_line" data-linenumber="617" 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">

617

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC617" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?subparaBlast=(.*)$/i</span><span class="p">)</span>  <span class="p">{</span> <span class="nv" style="color: #008080;">$blastOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="616" 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">

616

</td>

<td class="diff-line-num new_line" data-linenumber="618" 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">

618

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC618" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?subparaCluster=(.*)$/i</span><span class="p">)</span>  <span class="p">{</span> <span class="nv" style="color: #008080;">$clusterOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$1</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="617" 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">

617

</td>

<td class="diff-line-num new_line" data-linenumber="619" 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">

619

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC619" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?v(ersion)?$/i</span><span class="p">)</span>  <span class="p">{</span> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">$version</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="618" 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">

618

</td>

<td class="diff-line-num new_line" data-linenumber="620" 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">

620

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC620" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">/^-/</span><span class="p">)</span>       <span class="p">{</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$files_map</span><span class="p">{</span><span class="nv" style="color: #008080;">$option</span><span class="p">})){</span><span class="nv" style="color: #008080;">$files_map</span><span class="p">{</span><span class="nv" style="color: #008080;">$option</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">,</span><span class="nv" style="color: #008080;">$option</span><span class="p">);}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> The input </span><span class="si" style="color: #d14;">$option</span><span class="s2" style="color: #d14;"> was is skipped, since it was allready given as input.</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Press 'strg+c' to prevent me from proceeding or wait 10 seconds to continue...</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="nb" style="color: #0086b3;">sleep</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Well then, proceeding...</span><span class="se" style="color: #d14;">\n</span><span class="p">"}</span> <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

619

</td>

<td class="diff-line-num new_line old" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC619" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?man$/i</span><span class="p">){</span> <span class="nv" style="color: #008080;"><span class="idiff left">pod2usage</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">exitstatus</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">verbose</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">)</span></span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

620

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<td class="diff-line-num new_line old" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC620" class="line" lang="perl">  <span class="k" style="font-weight: 600;">else</span>  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span> <span class="p">"</span><span class="s2" style="color: #d14;"><span class="idiff left">Invalid command line option: </span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="si" style="color: #d14;"><span class="idiff">$option</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff right">'!</span></span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

621

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<pre style="margin: 0;">+<span id="LC621" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?man$/i</span><span class="p">){</span> <span class="k" style="font-weight: 600;"><span class="idiff left">my</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$bperldoc</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="p"><span class="idiff">(`</span></span><span class="sb" style="color: #d14;"><span class="idiff">perldoc -l Pod::Usage 2>&1</span></span><span class="p"><span class="idiff">`</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=~</span></span><span class="sr" style="color: #009926;"><span class="idiff">m/need to install/</span></span><span class="p"><span class="idiff">));</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="nv" style="color: #008080;"><span class="idiff">$bperldoc</span></span><span class="idiff"> </span><span class="p"><span class="idiff">){</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">You need to install the perl-doc package to use this man program.</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="p"><span class="idiff">";</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">pod2usage</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">exitstatus</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: #008080;"><span class="idiff">verbose</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">exit</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

622

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<pre style="margin: 0;">+<span id="LC622" class="line" lang="perl">  <span class="k" style="font-weight: 600;">else</span>  <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">print_usage</span><span class="p">();</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span> <span class="p">"</span><span class="si" style="color: #d14;"><span class="idiff left">$RED</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">[Error]</span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="si" style="color: #d14;"><span class="idiff">$ORANGE</span></span><span class="s2" style="color: #d14;"><span class="idiff"> Invalid command line option: </span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">'</span></span><span class="si" style="color: #d14;"><span class="idiff">$option</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="s2" style="color: #d14;"><span class="idiff">'! </span></span><span class="si" style="color: #d14;"><span class="idiff">$NC</span></span><span class="se" style="color: #d14;"><span class="idiff right">\n</span>\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="621" 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">

621

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<td class="diff-line-num new_line" data-linenumber="623" 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">

623

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="perl"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="622" 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">

622

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<td class="diff-line-num new_line" data-linenumber="624" 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">

624

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="623" 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">

623

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<td class="diff-line-num new_line" data-linenumber="625" 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">

625

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$selfblast</span><span class="p">){</span><span class="nv" style="color: #008080;">$checkblast</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="628" 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">@@ -626,7 +628,7 @@ $po_path = &get_po_path();    # Determine local path</td>

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<td class="diff-line-num old_line" data-linenumber="626" 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">

626

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<td class="diff-line-num new_line" data-linenumber="628" 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">

628

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<pre style="margin: 0;"> <span id="LC628" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="627" 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">

627

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<td class="diff-line-num new_line" data-linenumber="629" 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">

629

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$nucleotideAlphabet</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">ACGTURYSWKMBDHVNXacgturyswkmbdhvnx</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">.</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">-</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="628" 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">

628

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<td class="diff-line-num new_line" data-linenumber="630" 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">

630

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$aminoAlphabet</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">XOUBZACDEFGHIKLMNPQRSTVWYxoubzacdefghiklmnpqrstvwy</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">.</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">*</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">-</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

629

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<td class="diff-line-num new_line old" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC629" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$allowedAlphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="631" style="width: 35px; color: rgba(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="LC631" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$allowedAlphabet</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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630

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632

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="perl">  <span class="p">'</span><span class="s1" style="color: #d14;">blastn_legacy</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">n</span><span class="p">'</span> <span class="p">,</span></span>

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631

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633

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="perl">  <span class="p">'</span><span class="s1" style="color: #d14;">blastp_legacy</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">a</span><span class="p">'</span> <span class="p">,</span></span>

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632

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634

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<pre style="margin: 0;"> <span id="LC634" class="line" lang="perl">  <span class="p">'</span><span class="s1" style="color: #d14;">tblastx</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">'</span><span class="s1" style="color: #d14;">n</span><span class="p">'</span> <span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="665" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="667" 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">@@ -665,7 +667,7 @@ my $restart_counter=-1; # restart only once</td>

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665

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Check parameters</span></span>

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$startat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: #008080;">$stopat</span><span class="p">))</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC668" class="line" lang="perl">  <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Sorry, -startat and -stopat were removed. Please use -jobs=M/N for more flexible job splitting.</span><span class="p">");</span><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="perl">  <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Sorry, -startat and -stopat were removed. Please use -jobs=M/N for more flexible job splitting.</span><span class="p">");</span></span>

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="perl"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="685" 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">@@ -683,7 +685,7 @@ if ($jobnumber != -1) {</td>

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<pre style="margin: 0;"> <span id="LC685" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$gccversionstr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">`</span><span class="sb" style="color: #d14;">gcc --version 2>/dev/null</span><span class="p">`;</span></span>

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<pre style="margin: 0;"> <span id="LC687" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$gccversion_main</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>

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<pre style="margin: 0;">-<span id="LC686" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC689" class="line" lang="perl">  <span class="nv" style="color: #008080;">$gccversion_main</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="nv" style="color: #008080;">$gccversionstr</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^[^\n]+ ([\d]+)\.[\d\.]+\n/</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="688" 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">

688

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<td class="diff-line-num new_line" data-linenumber="690" 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">

690

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<pre style="margin: 0;"> <span id="LC690" class="line" lang="perl"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="689" 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">

689

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<td class="diff-line-num new_line" data-linenumber="691" 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">

691

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<pre style="margin: 0;"> <span id="LC691" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: #008080;">$ompprocbind</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="s2" style="color: #d14;">close</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="786" 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">@@ -784,10 +786,10 @@ if ($step == 0 || $step == 1) {</td>

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784

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<td class="diff-line-num new_line" data-linenumber="786" 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">

786

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<pre style="margin: 0;"> <span id="LC786" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="785" 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">

785

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<td class="diff-line-num new_line" data-linenumber="787" 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">

787

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<pre style="margin: 0;"> <span id="LC787" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Step 2, run blast and synteny algorithm</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC788" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

787

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<td class="diff-line-num new_line old" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC787" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="s2" style="color: #d14;">**Step 2**</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> using </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> </span><span class="p">";</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="789" style="width: 35px; color: rgba(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="LC789" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="si" style="color: #d14;">$GREEN</span><span class="s2" style="color: #d14;">**Step 2**</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> using </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> </span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="790" 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">

790

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<pre style="margin: 0;"> <span id="LC790" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$synteny</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$selfblast</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">with :</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC791" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$synteny</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> synteny</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

790

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<td class="diff-line-num new_line old" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC790" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$selfblast</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> selfblast</span><span class="p">";}</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="792" style="width: 35px; color: rgba(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="LC792" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$selfblast</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"> selfblast</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC793" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC794" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC795" class="line" lang="perl">  <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">init_graph_output</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Initiate Output file(s)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="876" 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">@@ -874,7 +876,7 @@ sub cluster {</td>

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874

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876

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<pre style="margin: 0;"> <span id="LC876" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Using MCL for clustering (-ram has no effect).</span><span class="si" style="color: #d14;">$NC</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span> <span class="c1" style="color: #998; font-style: italic;"># minimum 5 MB</span></span>

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<td class="diff-line-num new_line" data-linenumber="877" 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">

877

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="878" 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">

878

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<pre style="margin: 0;"> <span id="LC878" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC877" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$useMcl</span><span class="p">){</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="879" style="width: 35px; color: rgba(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="LC879" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$useMcl</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="878" 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">

878

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<td class="diff-line-num new_line" data-linenumber="880" 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">

880

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<pre style="margin: 0;"> <span id="LC880" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span> <span class="p">("</span><span class="s2" style="color: #d14;">OMP_PROC_BIND=</span><span class="si" style="color: #d14;">$ompprocbind</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_clustering -minspecies </span><span class="si" style="color: #d14;">$minspecies</span><span class="s2" style="color: #d14;"> -ram </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$freemem_inMB</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -kmere </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">$exactstep3</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> -debug </span><span class="si" style="color: #d14;">$debug</span><span class="s2" style="color: #d14;"> -cpus </span><span class="si" style="color: #d14;">$cpus</span><span class="s2" style="color: #d14;"> -weighted 1 -verbose </span><span class="si" style="color: #d14;">$verbose</span><span class="s2" style="color: #d14;"> -conn </span><span class="si" style="color: #d14;">$connectivity</span><span class="s2" style="color: #d14;"> -purity </span><span class="si" style="color: #d14;">$purity</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$clusterOptions</span><span class="s2" style="color: #d14;"> -rmgraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' </span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">* >'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC881" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="880" 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">

880

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<td class="diff-line-num new_line" data-linenumber="882" 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">

882

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<pre style="margin: 0;"> <span id="LC882" class="line" lang="perl">          <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">proteinortho_clustering failed. Did you use the static version?</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Maybe your operating system does not support the statically compiled version, please try recompiling proteinortho with 'make clean' and 'make' (and 'make install PREFIX=...').</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="891" 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">@@ -889,14 +891,17 @@ sub cluster {</td>

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<td class="diff-line-num old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC891" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">mv mcl.proteinortho-graph </span><span class="si" style="color: #d14;">$csimgraph</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC892" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="891" 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">

891

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<td class="diff-line-num new_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC893" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC892" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$simtable</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> You can extract the fasta files of each orthology group with 'proteinortho_grab_proteins.pl -tofiles </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> (Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

894

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<pre style="margin: 0;">+<span id="LC894" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$simtable</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="895" style="width: 35px; color: rgba(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="LC895" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

896

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<pre style="margin: 0;">+<span id="LC896" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with 'proteinortho_grab_proteins.pl -tofiles </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> (Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

897

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC897" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="893" 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">

893

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<td class="diff-line-num new_line" data-linenumber="898" 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">

898

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC898" class="line" lang="perl">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="894" 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">

894

</td>

<td class="diff-line-num new_line" data-linenumber="899" 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">

899

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<pre style="margin: 0;"> <span id="LC899" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$singles</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="895" 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">

895

</td>

<td class="diff-line-num new_line" data-linenumber="900" 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">

900

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<pre style="margin: 0;"> <span id="LC900" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Adding singles...</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="896" 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">

896

</td>

<td class="diff-line-num new_line" data-linenumber="901" 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">

901

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<pre style="margin: 0;"> <span id="LC901" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$fastas</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="897" 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">

897

</td>

<td class="diff-line-num new_line" data-linenumber="902" 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">

902

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<pre style="margin: 0;"> <span id="LC902" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_singletons.pl </span><span class="si" style="color: #d14;">$fastas</span><span class="s2" style="color: #d14;"> <'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">' >>'</span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="898" 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">

898

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<td class="diff-line-num new_line" data-linenumber="903" 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">

903

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC903" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

899

</td>

<td class="diff-line-num new_line old" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC899" class="line" lang="perl"><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

904

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC904" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="900" 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">

900

</td>

<td class="diff-line-num new_line" data-linenumber="905" 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">

905

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC905" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$nograph</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$useMcl</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="901" 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">

901

</td>

<td class="diff-line-num new_line" data-linenumber="906" 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">

906

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC906" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_graphMinusRemovegraph '</span><span class="si" style="color: #d14;">$rm_simgraph</span><span class="s2" style="color: #d14;">' </span><span class="si" style="color: #d14;">$simgraph</span><span class="s2" style="color: #d14;">* >'</span><span class="si" style="color: #d14;">$csimgraph</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="902" 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">

902

</td>

<td class="diff-line-num new_line" data-linenumber="907" 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">

907

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC907" class="line" lang="perl">    <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: #008080;">$keep</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: #008080;">$rm_simgraph</span><span class="p">);}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="910" 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">@@ -905,8 +910,12 @@ sub cluster {</td>

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<td class="diff-line-num old_line" data-linenumber="905" 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">

905

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<td class="diff-line-num new_line" data-linenumber="910" 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">

910

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<pre style="margin: 0;"> <span id="LC910" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous pairs are written to </span><span class="si" style="color: #d14;">$csimgraph</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="906" 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">

906

</td>

<td class="diff-line-num new_line" data-linenumber="911" 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">

911

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC911" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="907" 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">

907

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<td class="diff-line-num new_line" data-linenumber="912" 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">

912

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC912" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

908

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<td class="diff-line-num new_line old" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC908" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">perl </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho2html.pl </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> ></span><span class="si" style="color: #d14;">$simtablehtml</span><span class="p">");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

909

</td>

<td class="diff-line-num new_line old" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC909" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$simtablehtml</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

913

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC913" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span> <span class="nv" style="color: #008080;">@files</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">10</span><span class="p">){</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

914

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC914" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">perl </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho2html.pl </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> ></span><span class="si" style="color: #d14;">$simtablehtml</span><span class="p">");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

915

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC915" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$simtablehtml</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

916

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC916" class="line" lang="perl">  <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

917

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC917" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> You can extract a html version of the output using :</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">proteinortho2html.pl </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> [PLACE FASTA FILES HERE] ></span><span class="si" style="color: #d14;">$simtablehtml</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

918

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC918" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="910" 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">

910

</td>

<td class="diff-line-num new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

919

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC919" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="911" 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">

911

</td>

<td class="diff-line-num new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

920

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC920" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$doxml</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="912" 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">

912

</td>

<td class="diff-line-num new_line" data-linenumber="921" 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">

921

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC921" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">perl </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho2xml.pl </span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;"> ></span><span class="si" style="color: #d14;">$simtable</span><span class="s2" style="color: #d14;">.xml</span><span class="p">");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -928,7 +937,7 @@ sub cluster {</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

928

</td>

<td class="diff-line-num new_line" data-linenumber="937" 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">

937

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC937" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

929

</td>

<td class="diff-line-num new_line" data-linenumber="938" 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">

938

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC938" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="930" 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">

930

</td>

<td class="diff-line-num new_line" data-linenumber="939" 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">

939

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC939" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">[OUTPUT] -> Orthologous groups are written to </span><span class="si" style="color: #d14;">$syntable</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">You can extract the fasta files of each orthology group with 'proteinortho_grab_proteins.pl -tofiles </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;"> </span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">(Careful: This will generate a file foreach line in the file </span><span class="si" style="color: #d14;">$syntable</span><span class="s2" style="color: #d14;">).</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

931

</td>

<td class="diff-line-num new_line old" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC931" class="line" lang="perl"><span class="idiff left right">    </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

940

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC940" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="932" 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">

932

</td>

<td class="diff-line-num new_line" data-linenumber="941" 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">

941

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC941" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$singles</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="933" 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">

933

</td>

<td class="diff-line-num new_line" data-linenumber="942" 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">

942

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC942" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Adding singles...</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="934" 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">

934

</td>

<td class="diff-line-num new_line" data-linenumber="943" 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">

943

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC943" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$fastas</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">("</span><span class="s2" style="color: #d14;">' '</span><span class="p">",</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">'</span><span class="p">";</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="971" 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">@@ -962,14 +971,14 @@ sub print_header {</td>

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<td class="diff-line-num old_line" data-linenumber="962" 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">

962

</td>

<td class="diff-line-num new_line" data-linenumber="971" 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">

971

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC971" class="line" lang="perl"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="963" 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">

963

</td>

<td class="diff-line-num new_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

972

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC972" class="line" lang="perl"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="964" 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">

964

</td>

<td class="diff-line-num new_line" data-linenumber="973" 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">

973

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC973" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">print_usage</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

965

</td>

<td class="diff-line-num new_line old" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC965" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;"><span class="idiff left right">      </span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

974

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC974" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="966" 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">

966

</td>

<td class="diff-line-num new_line" data-linenumber="975" 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">

975

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC975" class="line" lang="perl"><span class="s2" style="color: #d14;">     |</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="967" 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">

967

</td>

<td class="diff-line-num new_line" data-linenumber="976" 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">

976

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC976" class="line" lang="perl"><span class="s2" style="color: #d14;">  </span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;">  /</span><span class="si" style="color: #d14;">${NC}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${RED2}</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">  </span><span class="si" style="color: #d14;">$NC</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="968" 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">

968

</td>

<td class="diff-line-num new_line" data-linenumber="977" 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">

977

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC977" class="line" lang="perl"><span class="s2" style="color: #d14;">  </span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;"> /</span><span class="se" style="color: #d14;">\\</span><span class="si" style="color: #d14;">${NC}${RED2}</span><span class="s2" style="color: #d14;"> /</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$NC</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="969" 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">

969

</td>

<td class="diff-line-num new_line" data-linenumber="978" 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">

978

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC978" class="line" lang="perl"><span class="s2" style="color: #d14;">  </span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;">/ </span><span class="si" style="color: #d14;">${RED2}</span><span class="s2" style="color: #d14;">/</span><span class="si" style="color: #d14;">${BLUE}</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${RED2}</span><span class="se" style="color: #d14;">\\</span><span class="si" style="color: #d14;">${NC}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="970" 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">

970

</td>

<td class="diff-line-num new_line" data-linenumber="979" 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">

979

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC979" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="971" 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">

971

</td>

<td class="diff-line-num new_line" data-linenumber="980" 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">

980

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC980" class="line" lang="perl"><span class="s2" style="color: #d14;">Usage: proteinortho6.pl [OPTIONS] FASTA1 FASTA2 [FASTA...] (one for each species, at least 2)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

972

</td>

<td class="diff-line-num new_line old" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC972" class="line" lang="perl"><span class="s2" style="color: #d14;">Options:<span class="idiff left right"> </span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

981

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC981" class="line" lang="perl"><span class="s2" style="color: #d14;">Options:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="973" 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">

973

</td>

<td class="diff-line-num new_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

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<pre style="margin: 0;"> <span id="LC982" class="line" lang="perl"><span class="s2" style="color: #d14;">         [General options]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="974" 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">

974

</td>

<td class="diff-line-num new_line" data-linenumber="983" 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">

983

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<pre style="margin: 0;"> <span id="LC983" class="line" lang="perl"><span class="s2" style="color: #d14;">         -project=    prefix for all result file names [default: myproject]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="975" 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">

975

</td>

<td class="diff-line-num new_line" data-linenumber="984" 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">

984

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<pre style="margin: 0;"> <span id="LC984" class="line" lang="perl"><span class="s2" style="color: #d14;">         -cpus=       number of processors to use [default: auto]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1000" 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">@@ -991,8 +1000,8 @@ Options:</td>

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<td class="diff-line-num old_line" data-linenumber="991" 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">

991

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<td class="diff-line-num new_line" data-linenumber="1000" 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">

1000

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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="perl"><span class="s2" style="color: #d14;">                      blast*+|tblastx+ : standard blastal family (blastp+ : protein files, blastn+ : dna files)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="992" 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">

992

</td>

<td class="diff-line-num new_line" data-linenumber="1001" 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">

1001

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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="perl"><span class="s2" style="color: #d14;">                      blast*_legacy : legacy blast family</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="993" 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">

993

</td>

<td class="diff-line-num new_line" data-linenumber="1002" 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">

1002

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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="perl"><span class="s2" style="color: #d14;">                      diamond : Only for protein files! standard diamond procedure and for genes/proteins of length >40 with the additional --sensitive flag</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

994

</td>

<td class="diff-line-num new_line old" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC994" class="line" lang="perl"><span class="s2" style="color: #d14;">                      usearch : usearch_local procedure with -id 0 (minimum identity percentage).<span class="idiff left right"> </span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

995

</td>

<td class="diff-line-num new_line old" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC995" class="line" lang="perl"><span class="s2" style="color: #d14;">                      ublast : usearch_ublast procedure.<span class="idiff left right"> </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1003

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1003" class="line" lang="perl"><span class="s2" style="color: #d14;">                      usearch : usearch_local procedure with -id 0 (minimum identity percentage).</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1004

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1004" class="line" lang="perl"><span class="s2" style="color: #d14;">                      ublast : usearch_ublast procedure.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="996" 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">

996

</td>

<td class="diff-line-num new_line" data-linenumber="1005" 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">

1005

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<pre style="margin: 0;"> <span id="LC1005" class="line" lang="perl"><span class="s2" style="color: #d14;">                      lastn : standard lastal. Only for dna files!</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="997" 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">

997

</td>

<td class="diff-line-num new_line" data-linenumber="1006" 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">

1006

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<pre style="margin: 0;"> <span id="LC1006" class="line" lang="perl"><span class="s2" style="color: #d14;">                      lastp : lastal using -p and BLOSUM62 scoring matrix. Only for protein files!</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="998" 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">

998

</td>

<td class="diff-line-num new_line" data-linenumber="1007" 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">

1007

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<pre style="margin: 0;"> <span id="LC1007" class="line" lang="perl"><span class="s2" style="color: #d14;">                      rapsearch : Only for protein files!</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1011" 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">@@ -1002,7 +1011,7 @@ Options:</td>

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<td class="diff-line-num old_line" data-linenumber="1002" 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">

1002

</td>

<td class="diff-line-num new_line" data-linenumber="1011" 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">

1011

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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="perl"><span class="s2" style="color: #d14;">         -e=          E-value for blast [default: 1e-05]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1003" 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">

1003

</td>

<td class="diff-line-num new_line" data-linenumber="1012" 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">

1012

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1012" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1004" 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">

1004

</td>

<td class="diff-line-num new_line" data-linenumber="1013" 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">

1013

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1013" class="line" lang="perl"><span class="s2" style="color: #d14;">         [Synteny options]</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1005

</td>

<td class="diff-line-num new_line old" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1005" class="line" lang="perl"><span class="s2" style="color: #d14;">         -synteny     activate PoFF extension to separate similar sequences</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1014

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1014" class="line" lang="perl"><span class="s2" style="color: #d14;">         -synteny     activate PoFF extension to separate similar sequences<span class="idiff left right"> print</span></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="1006" 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">

1006

</td>

<td class="diff-line-num new_line" data-linenumber="1015" 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">

1015

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1015" class="line" lang="perl"><span class="s2" style="color: #d14;">                      by contextual adjacencies (requires .gff for each .fasta)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1007" 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">

1007

</td>

<td class="diff-line-num new_line" data-linenumber="1016" 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">

1016

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1016" class="line" lang="perl"><span class="s2" style="color: #d14;">         -dups=       PoFF: number of reiterations for adjacencies heuristic,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1008" 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">

1008

</td>

<td class="diff-line-num new_line" data-linenumber="1017" 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">

1017

</td>

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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="perl"><span class="s2" style="color: #d14;">                      to determine duplicated regions (default: 0)</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1026" 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">@@ -1017,7 +1026,7 @@ Options:</td>

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<td class="diff-line-num old_line" data-linenumber="1017" 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">

1017

</td>

<td class="diff-line-num new_line" data-linenumber="1026" 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">

1026

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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="perl"><span class="s2" style="color: #d14;">         -xml        produces an OrthoXML formatted file of the *.proteinortho.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1018" 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">

1018

</td>

<td class="diff-line-num new_line" data-linenumber="1027" 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">

1027

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1027" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1019" 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">

1019

</td>

<td class="diff-line-num new_line" data-linenumber="1028" 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">

1028

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1028" class="line" lang="perl"><span class="s2" style="color: #d14;">         (...)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1020

</td>

<td class="diff-line-num new_line old" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="perl"><span class="s2" style="color: #d14;"><span class="idiff left right">        </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1029

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1029" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1021" 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">

1021

</td>

<td class="diff-line-num new_line" data-linenumber="1030" 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">

1030

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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="perl"><span class="s2" style="color: #d14;">For more information see the man page: 'proteinortho -man' or online: https://gitlab.com/paulklemm_PHD/proteinortho</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1022" 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">

1022

</td>

<td class="diff-line-num new_line" data-linenumber="1031" 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">

1031

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1031" class="line" lang="perl"><span class="s2" style="color: #d14;">Or you can use the GUI proteinorthoHelper.html (available at http://lechnerlab.de/proteinortho/)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1023" 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">

1023

</td>

<td class="diff-line-num new_line" data-linenumber="1032" 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">

1032

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1032" class="line" lang="perl"><span class="s2" style="color: #d14;">Dou have suggestions or need more help: write a mail to lechner</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">@staff</span><span class="s2" style="color: #d14;">.uni-marburg.de.</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1097" 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">@@ -1088,7 +1097,7 @@ sub run_blast {</td>

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<td class="diff-line-num old_line" data-linenumber="1088" 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">

1088

</td>

<td class="diff-line-num new_line" data-linenumber="1097" 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">

1097

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1097" class="line" lang="perl"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1089" 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">

1089

</td>

<td class="diff-line-num new_line" data-linenumber="1098" 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">

1098

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1098" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># Spawn worker threads</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1090" 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">

1090

</td>

<td class="diff-line-num new_line" data-linenumber="1099" 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">

1099

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1099" class="line" lang="perl">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$cpus</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">create</span><span class="p">('</span><span class="s1" style="color: #d14;">workerthread</span><span class="p">');}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1091

</td>

<td class="diff-line-num new_line old" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1091" class="line" lang="perl"><span class="idiff left right">  </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1092" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1100

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1100" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1092" 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">

1092

</td>

<td class="diff-line-num new_line" data-linenumber="1101" 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">

1101

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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># For each file against each other file</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1093" 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">

1093

</td>

<td class="diff-line-num new_line" data-linenumber="1102" 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">

1102

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1102" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$job_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1094" 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">

1094

</td>

<td class="diff-line-num new_line" data-linenumber="1103" 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">

1103

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1103" class="line" lang="perl">  <span class="nv" style="color: #008080;">SPEC:</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nv" style="color: #008080;">$selfblast</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1126" 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">@@ -1117,6 +1126,8 @@ sub workerthread {</td>

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<td class="diff-line-num old_line" data-linenumber="1117" 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">

1117

</td>

<td class="diff-line-num new_line" data-linenumber="1126" 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">

1126

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1126" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$thread_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tid</span><span class="p">();</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1118" 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">

1118

</td>

<td class="diff-line-num new_line" data-linenumber="1127" 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">

1127

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1127" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$temp_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$tmp_path$project</span><span class="s2" style="color: #d14;">-</span><span class="si" style="color: #d14;">$run_id</span><span class="s2" style="color: #d14;">-</span><span class="si" style="color: #d14;">$thread_id</span><span class="p">";</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1119" 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">

1119

</td>

<td class="diff-line-num new_line" data-linenumber="1128" 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">

1128

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1128" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1129

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1129" class="line" lang="perl">  <span class="nv" style="color: #008080;">$temp_file</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/^\.\///</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1130

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1130" class="line" lang="perl"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1120" 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">

1120

</td>

<td class="diff-line-num new_line" data-linenumber="1131" 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">

1131

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1131" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># Clean up, just to be safe</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1121" 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">

1121

</td>

<td class="diff-line-num new_line" data-linenumber="1132" 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">

1132

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1132" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">unlink</span><span class="p">("</span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">");</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1122" 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">

1122

</td>

<td class="diff-line-num new_line" data-linenumber="1133" 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">

1133

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1133" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">unlink</span><span class="p">("</span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.log</span><span class="p">");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1170" 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">@@ -1159,7 +1170,7 @@ sub workerthread {</td>

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<td class="diff-line-num old_line" data-linenumber="1159" 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">

1159

</td>

<td class="diff-line-num new_line" data-linenumber="1170" 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">

1170

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1170" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Work</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1160" 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">

1160

</td>

<td class="diff-line-num new_line" data-linenumber="1171" 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">

1171

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1171" class="line" lang="perl">    <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">set_threads_per_process</span><span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">list</span><span class="p">()));</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1161" 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">

1161

</td>

<td class="diff-line-num new_line" data-linenumber="1172" 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">

1172

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1172" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$result_ij</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">blast</span><span class="p">(</span><span class="nv" style="color: #008080;">$file_i</span><span class="p">,</span><span class="nv" style="color: #008080;">$file_j</span><span class="p">,</span><span class="nv" style="color: #008080;">$thread_id</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1162

</td>

<td class="diff-line-num new_line old" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1162" class="line" lang="perl"><span class="idiff left right">  </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1173

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1173" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1163" 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">

1163

</td>

<td class="diff-line-num new_line" data-linenumber="1174" 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">

1174

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1174" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$result_ji</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1164" 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">

1164

</td>

<td class="diff-line-num new_line" data-linenumber="1175" 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">

1175

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1175" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$file_i</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$file_j</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1165" 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">

1165

</td>

<td class="diff-line-num new_line" data-linenumber="1176" 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">

1176

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1176" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># One run is enough (selfblast)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1200" 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">@@ -1189,10 +1200,9 @@ sub workerthread {</td>

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<td class="diff-line-num old_line" data-linenumber="1189" 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">

1189

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<td class="diff-line-num new_line" data-linenumber="1200" 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">

1200

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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: #008080;">PREGRAPH</span><span class="p">,"</span><span class="s2" style="color: #d14;">>></span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">")</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">Could not open temp file '</span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.tmp': $!</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1190" 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">

1190

</td>

<td class="diff-line-num new_line" data-linenumber="1201" 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">

1201

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<pre style="margin: 0;"> <span id="LC1201" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: #008080;">PREGRAPH</span> <span class="nv" style="color: #008080;">$ordered_matches</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1191" 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">

1191

</td>

<td class="diff-line-num new_line" data-linenumber="1202" 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">

1202

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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: #008080;">PREGRAPH</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1192

</td>

<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1192" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_ffadj_mcs.py '</span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.tmp' </span><span class="si" style="color: #d14;">$alpha</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1193

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<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1193" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$duplication</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1194

</td>

<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1194" class="line" lang="perl">        <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;"> --repeat-matching </span><span class="si" style="color: #d14;">$duplication</span><span class="s2" style="color: #d14;"> --min-cs-size </span><span class="si" style="color: #d14;">$cs</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1195

</td>

<td class="diff-line-num new_line old" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1195" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1203

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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ffadj_param</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">-a </span><span class="si" style="color: #d14;">$alpha</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1204

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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$duplication</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: #008080;">$ffadj_param</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;"> -R </span><span class="si" style="color: #d14;">$duplication</span><span class="s2" style="color: #d14;"> -M </span><span class="si" style="color: #d14;">$cs</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1205

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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_ffadj_mcs.py </span><span class="si" style="color: #d14;">$ffadj_param</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$temp_file</span><span class="s2" style="color: #d14;">.tmp'</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1196" 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">

1196

</td>

<td class="diff-line-num new_line" data-linenumber="1206" 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">

1206

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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$cmd</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1197" 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">

1197

</td>

<td class="diff-line-num new_line" data-linenumber="1207" 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">

1207

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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$synt_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qx($cmd)</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1198" 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">

1198

</td>

<td class="diff-line-num new_line" data-linenumber="1208" 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">

1208

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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="perl">      <span class="nv" style="color: #008080;">$synt_stats</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1228" 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">@@ -1218,11 +1228,13 @@ sub workerthread {</td>

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<td class="diff-line-num old_line" data-linenumber="1218" 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">

1218

</td>

<td class="diff-line-num new_line" data-linenumber="1228" 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">

1228

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<pre style="margin: 0;"> <span id="LC1228" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nb" style="color: #0086b3;">close</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">%</span><span class="p">{</span><span class="nv" style="color: #008080;">$close_copies_pointer</span><span class="p">};</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1219" 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">

1219

</td>

<td class="diff-line-num new_line" data-linenumber="1229" 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">

1229

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1229" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;"># Generate hash for synteny hits</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1220" 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">

1220

</td>

<td class="diff-line-num new_line" data-linenumber="1230" 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">

1230

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1230" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">synteny</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1231

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1231" class="line" lang="perl"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1221" 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">

1221

</td>

<td class="diff-line-num new_line" data-linenumber="1232" 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">

1232

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1232" class="line" lang="perl">      <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="sr" style="color: #009926;">s "$temp_file.matching") {</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1222

</td>

<td class="diff-line-num new_line old" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1222" class="line" lang="perl"><span class="sr" style="color: #009926;">        print STDERR "</span><span class="nv" style="color: #008080;"><span class="idiff left">$RED</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Error</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Failed</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">to</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">run</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$po_path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nv" style="color: #008080;"><span class="idiff">proteinortho_ffadj_mcs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">py</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="o" style="font-weight: 600;"><span class="idiff">\</span></span><span class="nv" style="color: #008080;"><span class="idiff">n$file_i</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">vs</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$file_j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">\</span></span><span class="nv" style="color: #008080;"><span class="idiff">nMoving</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">source</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">to</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$temp_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">err</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">debugging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">\</span></span><span class="nv" style="color: #008080;"><span class="idiff">nI</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">will</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">continue</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">but</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">results</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">may</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">be</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">insufficient</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$NC</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">n</span><span class="p">"</span><span class="s2" style="color: #d14;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1233

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1233" class="line" lang="perl"><span class="sr" style="color: #009926;">        print STDERR "</span><span class="o" style="font-weight: 600;"><span class="idiff left">\</span></span><span class="nv" style="color: #008080;"><span class="idiff">n$RED</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Error</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">Failed</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">to</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">run</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$po_path</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="nv" style="color: #008080;"><span class="idiff">proteinortho_ffadj_mcs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">py</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="o" style="font-weight: 600;"><span class="idiff">\</span></span><span class="nv" style="color: #008080;"><span class="idiff">n$file_i</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">vs</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$file_j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">\</span></span><span class="nv" style="color: #008080;"><span class="idiff">nMoving</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">source</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">to</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$temp_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">err</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">debugging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">\</span></span><span class="nv" style="color: #008080;"><span class="idiff">nI</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">will</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">continue</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">but</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">results</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">may</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">be</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">insufficient</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$NC</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">\</span></span><span class="nv" style="color: #008080;"><span class="idiff right">n</span></span><span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">n</span><span class="p">"</span><span class="s2" style="color: #d14;">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1223" 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">

1223

</td>

<td class="diff-line-num new_line" data-linenumber="1234" 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">

1234

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1234" class="line" lang="perl"><span class="s2" style="color: #d14;">        system(</span><span class="p">"</span><span class="nv" style="color: #008080;">mv</span> <span class="nv" style="color: #008080;">$temp_file</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">tmp</span> <span class="nv" style="color: #008080;">$temp_file</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">err</span><span class="p">"</span><span class="s2" style="color: #d14;">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1224" 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">

1224

</td>

<td class="diff-line-num new_line" data-linenumber="1235" 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">

1235

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1235" class="line" lang="perl"><span class="s2" style="color: #d14;">        next;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1225" 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">

1225

</td>

<td class="diff-line-num new_line" data-linenumber="1236" 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">

1236

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1236" class="line" lang="perl"><span class="s2" style="color: #d14;">      }</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1237

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1237" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1226" 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">

1226

</td>

<td class="diff-line-num new_line" data-linenumber="1238" 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">

1238

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1238" class="line" lang="perl"><span class="s2" style="color: #d14;">      open(OSYNGRAPH,</span><span class="p">"</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: #008080;">$temp_file</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">matching</span><span class="p">"</span><span class="s2" style="color: #d14;">) || &Error(</span><span class="p">"</span><span class="nv" style="color: #008080;">Could</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">open</span> <span class="nv" style="color: #008080;">temp</span> <span class="nv" style="color: #008080;">file</span> <span class="nv" style="color: #008080;">$temp_file</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">matching:</span> <span class="vg" style="color: #008080;">$!</span><span class="p">'</span><span class="s1" style="color: #d14;">");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1227" 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">

1227

</td>

<td class="diff-line-num new_line" data-linenumber="1239" 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">

1239

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1239" class="line" lang="perl"><span class="s1" style="color: #d14;">      while(<OSYNGRAPH>) {</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1228" 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">

1228

</td>

<td class="diff-line-num new_line" data-linenumber="1240" 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">

1240

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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="perl"><span class="s1" style="color: #d14;">          $_=~s/[</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s1" style="color: #d14;">r</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s1" style="color: #d14;">n]+$//;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1510,7 +1522,7 @@ sub print_blast_stats {</td>

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<td class="diff-line-num old_line" data-linenumber="1510" 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">

1510

</td>

<td class="diff-line-num new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1522

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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="perl"><span class="s1" style="color: #d14;">    lock($jobs_done);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1511" 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">

1511

</td>

<td class="diff-line-num new_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1523

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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="perl"><span class="s1" style="color: #d14;">    my $percent = int($jobs_done/$jobs_todo*10000)/100;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1512" 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">

1512

</td>

<td class="diff-line-num new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1524

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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="perl"><span class="s1" style="color: #d14;">    print STDERR "</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s1" style="color: #d14;">r                                                                               ";</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1513

</td>

<td class="diff-line-num new_line old" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1513" class="line" lang="perl"><span class="s1" style="color: #d14;"><span class="idiff left right">  </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1525

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1525" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1514" 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">

1514

</td>

<td class="diff-line-num new_line" data-linenumber="1526" 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">

1526

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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="perl"><span class="s1" style="color: #d14;">    if ($split_to_X_jobs == -1) {</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1515" 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">

1515

</td>

<td class="diff-line-num new_line" data-linenumber="1527" 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">

1527

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<pre style="margin: 0;"> <span id="LC1527" class="line" lang="perl"><span class="s1" style="color: #d14;">      print STDERR "</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s1" style="color: #d14;">rRunning blast analysis: $percent% ($jobs_done/$jobs_todo)";</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1516" 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">

1516

</td>

<td class="diff-line-num new_line" data-linenumber="1528" 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">

1528

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1528" class="line" lang="perl"><span class="s1" style="color: #d14;">    }</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1585" 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">@@ -1573,7 +1585,7 @@ sub get_legal_matches {</td>

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<td class="diff-line-num old_line" data-linenumber="1573" 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">

1573

</td>

<td class="diff-line-num new_line" data-linenumber="1585" 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">

1585

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<pre style="margin: 0;"> <span id="LC1585" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># if(($blastmode ne "phmmer" && $blastmode ne "jackhmmer")){ #workaround for jackhmmer + phmmer</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1574" 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">

1574

</td>

<td class="diff-line-num new_line" data-linenumber="1586" 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">

1586

</td>

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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Percent identity</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1575" 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">

1575

</td>

<td class="diff-line-num new_line" data-linenumber="1587" 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">

1587

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1587" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$twilight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$local_identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$identity</span><span class="p">)</span>          <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1576

</td>

<td class="diff-line-num new_line old" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1576" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$twilight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$local_identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">identitybylength</span><span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span><span class="p">))</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1588

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1588" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="nv" style="color: #008080;">$twilight</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$local_identity</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">identitybylength</span><span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span><span class="p">))</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1577" 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">

1577

</td>

<td class="diff-line-num new_line" data-linenumber="1589" 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">

1589

</td>

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<pre style="margin: 0;"> <span id="LC1589" class="line" lang="perl">    <span class="c1" style="color: #998; font-style: italic;"># Min. length</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1578" 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">

1578

</td>

<td class="diff-line-num new_line" data-linenumber="1590" 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">

1590

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1590" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx+</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">tblastx</span><span class="p">")</span> <span class="p">{</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">3</span><span class="p">;}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1579" 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">

1579

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<td class="diff-line-num new_line" data-linenumber="1591" 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">

1591

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<pre style="margin: 0;"> <span id="LC1591" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$length</span><span class="p">{</span><span class="nv" style="color: #008080;">$query_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: #008080;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span>     <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1646" 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">@@ -1634,7 +1646,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1634" 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">

1634

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<td class="diff-line-num new_line" data-linenumber="1646" 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">

1646

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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1635" 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">

1635

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<td class="diff-line-num new_line" data-linenumber="1647" 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">

1647

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<pre style="margin: 0;"> <span id="LC1647" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1636" 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">

1636

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<td class="diff-line-num new_line" data-linenumber="1648" 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">

1648

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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1637

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<td class="diff-line-num new_line old" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1637" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1649

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<pre style="margin: 0;">+<span id="LC1649" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1638" 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">

1638

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<td class="diff-line-num new_line" data-linenumber="1650" 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">

1650

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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1639" 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">

1639

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<td class="diff-line-num new_line" data-linenumber="1651" 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">

1651

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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1640" 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">

1640

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<td class="diff-line-num new_line" data-linenumber="1652" 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">

1652

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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1665" 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">@@ -1653,7 +1665,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1653" 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">

1653

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<td class="diff-line-num new_line" data-linenumber="1665" 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">

1665

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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\s/</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">File name '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' contains whitespaces. This might lead to undesired effects. If you encounter unusual behaviours, please change the file name!</span><span class="se" style="color: #d14;">\n</span><span class="p">");}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1654" 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">

1654

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<td class="diff-line-num new_line" data-linenumber="1666" 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">

1666

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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1655" 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">

1655

</td>

<td class="diff-line-num new_line" data-linenumber="1667" 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">

1667

</td>

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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1656

</td>

<td class="diff-line-num new_line old" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1656" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1668

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1668" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1657" 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">

1657

</td>

<td class="diff-line-num new_line" data-linenumber="1669" 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">

1669

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<pre style="margin: 0;"> <span id="LC1669" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1658" 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">

1658

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<td class="diff-line-num new_line" data-linenumber="1670" 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">

1670

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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -d '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' --quiet ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1659" 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">

1659

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<td class="diff-line-num new_line" data-linenumber="1671" 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">

1671

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<pre style="margin: 0;"> <span id="LC1671" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1685" 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">@@ -1673,7 +1685,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1673" 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">

1673

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<td class="diff-line-num new_line" data-linenumber="1685" 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">

1685

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1685" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1674" 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">

1674

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<td class="diff-line-num new_line" data-linenumber="1686" 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">

1686

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<pre style="margin: 0;"> <span id="LC1686" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1675" 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">

1675

</td>

<td class="diff-line-num new_line" data-linenumber="1687" 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">

1687

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<pre style="margin: 0;"> <span id="LC1687" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1676

</td>

<td class="diff-line-num new_line old" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1676" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1688

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1688" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1677" 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">

1677

</td>

<td class="diff-line-num new_line" data-linenumber="1689" 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">

1689

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1689" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1678" 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">

1678

</td>

<td class="diff-line-num new_line" data-linenumber="1690" 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">

1690

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<pre style="margin: 0;"> <span id="LC1690" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> index -f '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1679" 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">

1679

</td>

<td class="diff-line-num new_line" data-linenumber="1691" 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">

1691

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<pre style="margin: 0;"> <span id="LC1691" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1705" 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">@@ -1693,7 +1705,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1693" 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">

1693

</td>

<td class="diff-line-num new_line" data-linenumber="1705" 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">

1705

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<pre style="margin: 0;"> <span id="LC1705" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1694" 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">

1694

</td>

<td class="diff-line-num new_line" data-linenumber="1706" 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">

1706

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<pre style="margin: 0;"> <span id="LC1706" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1695" 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">

1695

</td>

<td class="diff-line-num new_line" data-linenumber="1707" 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">

1707

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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1696

</td>

<td class="diff-line-num new_line old" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1696" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1708

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<pre style="margin: 0;">+<span id="LC1708" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1697" 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">

1697

</td>

<td class="diff-line-num new_line" data-linenumber="1709" 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">

1709

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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1698" 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">

1698

</td>

<td class="diff-line-num new_line" data-linenumber="1710" 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">

1710

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1710" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 1 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1699" 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">

1699

</td>

<td class="diff-line-num new_line" data-linenumber="1711" 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">

1711

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1711" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1725" 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">@@ -1713,7 +1725,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1713" 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">

1713

</td>

<td class="diff-line-num new_line" data-linenumber="1725" 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">

1725

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1725" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1714" 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">

1714

</td>

<td class="diff-line-num new_line" data-linenumber="1726" 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">

1726

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<pre style="margin: 0;"> <span id="LC1726" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1715" 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">

1715

</td>

<td class="diff-line-num new_line" data-linenumber="1727" 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">

1727

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1727" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1716

</td>

<td class="diff-line-num new_line old" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1716" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1728

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1728" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1717" 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">

1717

</td>

<td class="diff-line-num new_line" data-linenumber="1729" 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">

1729

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1729" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1718" 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">

1718

</td>

<td class="diff-line-num new_line" data-linenumber="1730" 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">

1730

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1730" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> --dbtype 2 '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1719" 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">

1719

</td>

<td class="diff-line-num new_line" data-linenumber="1731" 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">

1731

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1731" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1736" 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">@@ -1724,16 +1736,16 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1724" 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">

1724

</td>

<td class="diff-line-num new_line" data-linenumber="1736" 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">

1736

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1736" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1725" 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">

1725

</td>

<td class="diff-line-num new_line" data-linenumber="1737" 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">

1737

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1737" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="vg" style="color: #008080;">$?</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span> <span class="nv" style="color: #008080;">$keep</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$oldkeep</span><span class="p">;</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">The database generation failed once again, please retry with 'sudo' or move the fasta files to a directory with write permissions. If this failes too, then there is something wrong with the fasta files or the version of </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> cannot handle the database generation. So please try one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- update </span><span class="si" style="color: #d14;">$blastmode</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider another blast algorithm (-p)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- consider to submitting (mailing) this case to incoming+paulklemm-phd-proteinortho-7278443-issue-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">@incoming</span><span class="s2" style="color: #d14;">.gitlab.com.</span><span class="p">");}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1726" 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">

1726

</td>

<td class="diff-line-num new_line" data-linenumber="1738" 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">

1738

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1738" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1727

</td>

<td class="diff-line-num new_line old" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1727" class="line" lang="perl">      <span class="p">}</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1739

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1739" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1728" 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">

1728

</td>

<td class="diff-line-num new_line" data-linenumber="1740" 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">

1740

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1740" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1729" 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">

1729

</td>

<td class="diff-line-num new_line" data-linenumber="1741" 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">

1741

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1741" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1730" 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">

1730

</td>

<td class="diff-line-num new_line" data-linenumber="1742" 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">

1742

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1742" class="line" lang="perl">  <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">usearch</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">ublast</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1731" 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">

1731

</td>

<td class="diff-line-num new_line" data-linenumber="1743" 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">

1743

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1743" class="line" lang="perl">    <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">(</span><span class="nv" style="color: #008080;">@_</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1732" 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">

1732

</td>

<td class="diff-line-num new_line" data-linenumber="1744" 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">

1744

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1744" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\s/</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">File name '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' contains whitespaces. This might lead to undesired effects. If you encounter unusual behaviours, please change the file name!</span><span class="se" style="color: #d14;">\n</span><span class="p">");}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1733

</td>

<td class="diff-line-num new_line old" data-linenumber="1745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1733" class="line" lang="perl"><span class="idiff left right">      </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1745

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1745" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1734" 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">

1734

</td>

<td class="diff-line-num new_line" data-linenumber="1746" 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">

1746

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1746" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1735" 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">

1735

</td>

<td class="diff-line-num new_line" data-linenumber="1747" 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">

1747

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1747" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1736

</td>

<td class="diff-line-num new_line old" data-linenumber="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1736" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1748

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1748" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1737" 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">

1737

</td>

<td class="diff-line-num new_line" data-linenumber="1749" 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">

1749

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1749" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1738" 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">

1738

</td>

<td class="diff-line-num new_line" data-linenumber="1750" 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">

1750

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1750" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -output '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null 2></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1739" 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">

1739

</td>

<td class="diff-line-num new_line" data-linenumber="1751" 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">

1751

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1751" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="si" style="color: #d14;">$ORANGE</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed to create a database. Most likely you don't have write permissions in the directory of the fasta files. I will now proceed with writing the database files to the DB/ directory in </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> (-tmp).</span><span class="p">");</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> Please ensure that you use -tmp=</span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> -keep for future analysis.</span><span class="si" style="color: #d14;">$NC</span><span class="p">";}</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1764" 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">@@ -1752,7 +1764,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1752" 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">

1752

</td>

<td class="diff-line-num new_line" data-linenumber="1764" 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">

1764

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<pre style="margin: 0;"> <span id="LC1764" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\s/</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">File name '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' contains whitespaces. This might lead to undesired effects. If you encounter unusual behaviours, please change the file name!</span><span class="se" style="color: #d14;">\n</span><span class="p">");}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1753" 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">

1753

</td>

<td class="diff-line-num new_line" data-linenumber="1765" 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">

1765

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1765" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1754" 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">

1754

</td>

<td class="diff-line-num new_line" data-linenumber="1766" 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">

1766

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1766" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1755

</td>

<td class="diff-line-num new_line old" data-linenumber="1767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1755" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1767

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1767" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1756" 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">

1756

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<td class="diff-line-num new_line" data-linenumber="1768" 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">

1768

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<pre style="margin: 0;"> <span id="LC1768" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1757" 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">

1757

</td>

<td class="diff-line-num new_line" data-linenumber="1769" 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">

1769

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<pre style="margin: 0;"> <span id="LC1769" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">lastp</span><span class="p">"){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1758" 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">

1758

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<td class="diff-line-num new_line" data-linenumber="1770" 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">

1770

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1770" class="line" lang="perl">          <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> -p '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="p">");</span></span>

</pre>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1798" 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">@@ -1786,7 +1798,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1786" 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">

1786

</td>

<td class="diff-line-num new_line" data-linenumber="1798" 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">

1798

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1798" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\s/</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">File name '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' contains whitespaces. This might lead to undesired effects. If you encounter unusual behaviours, please change the file name!</span><span class="se" style="color: #d14;">\n</span><span class="p">");}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1787" 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">

1787

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<td class="diff-line-num new_line" data-linenumber="1799" 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">

1799

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1799" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1788" 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">

1788

</td>

<td class="diff-line-num new_line" data-linenumber="1800" 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">

1800

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1800" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1789

</td>

<td class="diff-line-num new_line old" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1789" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1801

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1801" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1790" 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">

1790

</td>

<td class="diff-line-num new_line" data-linenumber="1802" 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">

1802

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1802" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1791" 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">

1791

</td>

<td class="diff-line-num new_line" data-linenumber="1803" 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">

1803

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<pre style="margin: 0;"> <span id="LC1803" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1792" 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">

1792

</td>

<td class="diff-line-num new_line" data-linenumber="1804" 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">

1804

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<pre style="margin: 0;"> <span id="LC1804" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1817" 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">@@ -1805,7 +1817,7 @@ sub generate_indices {</td>

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<td class="diff-line-num old_line" data-linenumber="1805" 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">

1805

</td>

<td class="diff-line-num new_line" data-linenumber="1817" 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">

1817

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<pre style="margin: 0;"> <span id="LC1817" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\s/</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">File name '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' contains whitespaces. This might lead to undesired effects. If you encounter unusual behaviours, please change the file name!</span><span class="se" style="color: #d14;">\n</span><span class="p">");}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1806" 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">

1806

</td>

<td class="diff-line-num new_line" data-linenumber="1818" 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">

1818

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<pre style="margin: 0;"> <span id="LC1818" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">("",</span><span class="nb" style="color: #0086b3;">glob</span><span class="p">("</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">*</span><span class="p">"))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1807" 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">

1807

</td>

<td class="diff-line-num new_line" data-linenumber="1819" 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">

1819

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<pre style="margin: 0;"> <span id="LC1819" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">The database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' is present and will be used</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1808

</td>

<td class="diff-line-num new_line old" data-linenumber="1820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1808" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1820

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1820" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1809" 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">

1809

</td>

<td class="diff-line-num new_line" data-linenumber="1821" 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">

1821

</td>

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<pre style="margin: 0;"> <span id="LC1821" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Building database for '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> sequences)</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1810" 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">

1810

</td>

<td class="diff-line-num new_line" data-linenumber="1822" 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">

1822

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1822" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -out '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1811" 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">

1811

</td>

<td class="diff-line-num new_line" data-linenumber="1823" 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">

1823

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1823" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$makedb</span><span class="s2" style="color: #d14;"> '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' -n '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">.</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">' ></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/dev</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">/null</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1904" 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">@@ -1892,7 +1904,7 @@ sub blast {</td>

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<td class="diff-line-num old_line" data-linenumber="1892" 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">

1892

</td>

<td class="diff-line-num new_line" data-linenumber="1904" 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">

1904

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1904" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1893" 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">

1893

</td>

<td class="diff-line-num new_line" data-linenumber="1905" 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">

1905

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1905" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># File does not exists yet or I am forced to rewrite it</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1894" 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">

1894

</td>

<td class="diff-line-num new_line" data-linenumber="1906" 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">

1906

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1906" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$bla</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$force</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1895

</td>

<td class="diff-line-num new_line old" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1895" class="line" lang="perl"><span class="idiff left right">    </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1907

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1907" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1896" 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">

1896

</td>

<td class="diff-line-num new_line" data-linenumber="1908" 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">

1908

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1908" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$bla</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$force</span><span class="p">)</span> <span class="p">{</span> <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="p">");</span> <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1897" 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">

1897

</td>

<td class="diff-line-num new_line" data-linenumber="1909" 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">

1909

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1909" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1898" 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">

1898

</td>

<td class="diff-line-num new_line" data-linenumber="1910" 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">

1910

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<pre style="margin: 0;"> <span id="LC1910" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$verbose</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="si" style="color: #d14;">$command</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span>                     <span class="c1" style="color: #998; font-style: italic;"># 5.16</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1915" 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">@@ -1903,7 +1915,7 @@ sub blast {</td>

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<td class="diff-line-num old_line" data-linenumber="1903" 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">

1903

</td>

<td class="diff-line-num new_line" data-linenumber="1915" 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">

1915

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1915" class="line" lang="perl">        <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> failed.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The most likely  errorsources of this are:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- no space left on device error.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- outdated </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">, please update </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> or consider another -p algorithm.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- the databases are missing. Maybe you ran --step=1 and removed the databases afterwards? Please rerun 'proteinortho --step=1 --force /path/to/fastas'</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">- maybe the fasta files are mixed nucleotide and aminoacid sequences or just not suited for </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">? (For example diamond only processes protein sequences) Try 'proteinortho --step=1 --check --force /path/to/fastas'.</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1904" 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">

1904

</td>

<td class="diff-line-num new_line" data-linenumber="1916" 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">

1916

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<pre style="margin: 0;"> <span id="LC1916" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1905" 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">

1905

</td>

<td class="diff-line-num new_line" data-linenumber="1917" 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">

1917

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1917" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">test_sort</span><span class="p">"){</span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="p">"</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp</span><span class="p">"</span><span class="o" style="font-weight: 600;">></span><span class="p">){</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^\t]+([,])[^\t]+[eE]/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="p">"</span><span class="s2" style="color: #d14;">found forbidden symbol '$1' at </span><span class="si" style="color: #d14;">$_</span><span class="s2" style="color: #d14;"> in </span><span class="si" style="color: #d14;">$bla</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">reset_locale</span><span class="p">();</span><span class="nb" style="color: #0086b3;">die</span><span class="p">;}}}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1906

</td>

<td class="diff-line-num new_line old" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1906" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.daa</span><span class="p">");</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1918

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1918" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.daa</span><span class="p">");</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1907" 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">

1907

</td>

<td class="diff-line-num new_line" data-linenumber="1919" 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">

1919

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1919" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1908" 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">

1908

</td>

<td class="diff-line-num new_line" data-linenumber="1920" 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">

1920

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1920" class="line" lang="perl">    <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">rapsearch</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1909" 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">

1909

</td>

<td class="diff-line-num new_line" data-linenumber="1921" 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">

1921

</td>

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<pre style="margin: 0;"> <span id="LC1921" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1936" 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">@@ -1924,8 +1936,8 @@ sub blast {</td>

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<td class="diff-line-num old_line" data-linenumber="1924" 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">

1924

</td>

<td class="diff-line-num new_line" data-linenumber="1936" 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">

1936

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<pre style="margin: 0;"> <span id="LC1936" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.aln</span><span class="p">");</span> <span class="c1" style="color: #998; font-style: italic;">#remove aln file</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1925" 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">

1925

</td>

<td class="diff-line-num new_line" data-linenumber="1937" 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">

1937

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<pre style="margin: 0;"> <span id="LC1937" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">touch </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.m8</span><span class="p">");</span> <span class="c1" style="color: #998; font-style: italic;"># rapsearch does not produces an output file if there are no hits found (<evalue threshold).</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1926" 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">

1926

</td>

<td class="diff-line-num new_line" data-linenumber="1938" 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">

1938

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<pre style="margin: 0;"> <span id="LC1938" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">tail -n +6 </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.m82 >'</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp'</span><span class="p">");</span> <span class="c1" style="color: #998; font-style: italic;"># remove head/comment lines of rapsearch</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1927

</td>

<td class="diff-line-num new_line old" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1927" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.m8</span><span class="p">");</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1928

</td>

<td class="diff-line-num new_line old" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC1928" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.m82</span><span class="p">");</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1939

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1939" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.m8</span><span class="p">");</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1940

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1940" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.m82</span><span class="p">");</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1929" 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">

1929

</td>

<td class="diff-line-num new_line" data-linenumber="1941" 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">

1941

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<pre style="margin: 0;"> <span id="LC1941" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1930" 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">

1930

</td>

<td class="diff-line-num new_line" data-linenumber="1942" 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">

1942

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1942" class="line" lang="perl">    <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">usearch</span><span class="p">"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">ublast</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1931" 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">

1931

</td>

<td class="diff-line-num new_line" data-linenumber="1943" 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">

1943

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1943" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1948" 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">@@ -1936,7 +1948,7 @@ sub blast {</td>

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<td class="diff-line-num old_line" data-linenumber="1936" 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">

1936

</td>

<td class="diff-line-num new_line" data-linenumber="1948" 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">

1948

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1948" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#system("perl $po_path/proteinortho_formatUsearch.pl $bla >'$bla.tmp_format'"); # problem with ublast/usearch: gene names include the description.</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1937" 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">

1937

</td>

<td class="diff-line-num new_line" data-linenumber="1949" 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">

1949

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1949" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#system("sort $bla.tmp_format -k12,12rg >'$bla.tmp'");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1938" 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">

1938

</td>

<td class="diff-line-num new_line" data-linenumber="1950" 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">

1950

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1950" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">perl </span><span class="si" style="color: #d14;">$po_path</span><span class="s2" style="color: #d14;">/proteinortho_formatUsearch.pl </span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;"> >'</span><span class="si" style="color: #d14;">$bla</span><span class="s2" style="color: #d14;">.tmp'</span><span class="p">");</span> <span class="c1" style="color: #998; font-style: italic;"># problem with ublast/usearch: gene names include the description.</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1939

</td>

<td class="diff-line-num new_line old" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1939" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#system("rm $bla.tmp_format");<span class="idiff left right"> </span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1951

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1951" class="line" lang="perl">      <span class="c1" style="color: #998; font-style: italic;">#system("rm $bla.tmp_format");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1940" 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">

1940

</td>

<td class="diff-line-num new_line" data-linenumber="1952" 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">

1952

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1952" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1941" 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">

1941

</td>

<td class="diff-line-num new_line" data-linenumber="1953" 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">

1953

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1953" class="line" lang="perl">    <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">topaz</span><span class="p">")</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1942" 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">

1942

</td>

<td class="diff-line-num new_line" data-linenumber="1954" 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">

1954

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1954" class="line" lang="perl">      <span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="si" style="color: #d14;">$command</span><span class="p">");</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2296" 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">@@ -2284,7 +2296,7 @@ sub read_details {</td>

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<td class="diff-line-num old_line" data-linenumber="2284" 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">

2284

</td>

<td class="diff-line-num new_line" data-linenumber="2296" 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">

2296

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2296" class="line" lang="perl"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2285" 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">

2285

</td>

<td class="diff-line-num new_line" data-linenumber="2297" 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">

2297

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2297" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$checkfasta</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span><span class="p">){</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2286" 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">

2286

</td>

<td class="diff-line-num new_line" data-linenumber="2298" 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">

2298

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2298" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$checkfasta</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$genelength</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">50</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">n</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$ATCGNoccurences</span><span class="sr" style="color: #009926;">/$genelength < 0.5) || ($allowedAlphabet->{$blastmode} eq "a" && $ATCGNoccurences/</span><span class="nv" style="color: #008080;">$genelength</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.8</span><span class="p">)))){</span><span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2287

</td>

<td class="diff-line-num new_line old" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2287" class="line" lang="perl"><span class="idiff left right">      </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2299

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2299" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2288" 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">

2288

</td>

<td class="diff-line-num new_line" data-linenumber="2300" 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">

2300

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2300" class="line" lang="perl">      <span class="nv" style="color: #008080;">$gene_counter</span><span class="p">{</span><span class="nv" style="color: #008080;">$file</span><span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2289" 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">

2289

</td>

<td class="diff-line-num new_line" data-linenumber="2301" 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">

2301

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2301" class="line" lang="perl">      <span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">#chomp only removes last \n newline, now also \r are removed and all occurences</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2290" 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">

2290

</td>

<td class="diff-line-num new_line" data-linenumber="2302" 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">

2302

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2302" class="line" lang="perl">      <span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2314" 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">@@ -2302,15 +2314,15 @@ sub read_details {</td>

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<td class="diff-line-num old_line" data-linenumber="2302" 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">

2302

</td>

<td class="diff-line-num new_line" data-linenumber="2314" 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">

2314

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<pre style="margin: 0;"> <span id="LC2314" class="line" lang="perl">      <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2303" 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">

2303

</td>

<td class="diff-line-num new_line" data-linenumber="2315" 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">

2315

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2315" class="line" lang="perl">      <span class="nv" style="color: #008080;">$ATCGNoccurences</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2304" 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">

2304

</td>

<td class="diff-line-num new_line" data-linenumber="2316" 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">

2316

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2316" class="line" lang="perl">      <span class="nv" style="color: #008080;">$genelength</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2305

</td>

<td class="diff-line-num new_line old" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2305" class="line" lang="perl"><span class="idiff left right">    </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2306

</td>

<td class="diff-line-num new_line old" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC2306" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2317

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2317" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2318

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<pre style="margin: 0;">+<span id="LC2318" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2307" 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">

2307

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<td class="diff-line-num new_line" data-linenumber="2319" 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">

2319

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<pre style="margin: 0;"> <span id="LC2319" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2308" 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">

2308

</td>

<td class="diff-line-num new_line" data-linenumber="2320" 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">

2320

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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="perl">      <span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\r\n]+$//</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">#chomp only removes last \n newline, now also \r are removed and all occurences</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2309" 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">

2309

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<td class="diff-line-num new_line" data-linenumber="2321" 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">

2321

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<pre style="margin: 0;"> <span id="LC2321" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$checkfasta</span><span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})){</span> <span class="c1" style="color: #998; font-style: italic;">#test if the current gene is valid or not (for blastalgorithms that require either amino or nucleotide sequences only)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2310" 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">

2310

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<td class="diff-line-num new_line" data-linenumber="2322" 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">

2322

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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="perl">          <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">a</span><span class="p">"){</span> <span class="c1" style="color: #998; font-style: italic;">#"a"= aminoacid sequence</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2311" 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">

2311

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<td class="diff-line-num new_line" data-linenumber="2323" 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">

2323

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<pre style="margin: 0;"> <span id="LC2323" class="line" lang="perl">            <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^$aminoAlphabet]/</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2312" 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">

2312

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<td class="diff-line-num new_line" data-linenumber="2324" 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">

2324

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<pre style="margin: 0;"> <span id="LC2324" class="line" lang="perl">              <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2313

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<td class="diff-line-num new_line old" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2313" class="line" lang="perl">            <span class="p">}</span><span class="idiff left right"> </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2325

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2325" class="line" lang="perl">            <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2314" 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">

2314

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<td class="diff-line-num new_line" data-linenumber="2326" 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">

2326

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<pre style="margin: 0;"> <span id="LC2326" class="line" lang="perl">          <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/[^$nucleotideAlphabet]/</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2315" 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">

2315

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<td class="diff-line-num new_line" data-linenumber="2327" 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">

2327

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<pre style="margin: 0;"> <span id="LC2327" class="line" lang="perl">              <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2316" 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">

2316

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<td class="diff-line-num new_line" data-linenumber="2328" 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">

2328

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2328" class="line" lang="perl">          <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2356" 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">@@ -2344,7 +2356,7 @@ sub read_details {</td>

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<td class="diff-line-num old_line" data-linenumber="2344" 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">

2344

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<td class="diff-line-num new_line" data-linenumber="2356" 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">

2356

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2356" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2345" 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">

2345

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<td class="diff-line-num new_line" data-linenumber="2357" 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">

2357

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<pre style="margin: 0;"> <span id="LC2357" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$checkfasta</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: #008080;">$genelength</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">50</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span> <span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">n</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$ATCGNoccurences</span><span class="sr" style="color: #009926;">/$genelength < 0.5) || ($allowedAlphabet->{$blastmode} eq "a" && $ATCGNoccurences/</span><span class="nv" style="color: #008080;">$genelength</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.8</span><span class="p">)))){</span><span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2346" 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">

2346

</td>

<td class="diff-line-num new_line" data-linenumber="2358" 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">

2358

</td>

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<pre style="margin: 0;"> <span id="LC2358" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$force</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$checkfasta</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2347

</td>

<td class="diff-line-num new_line old" data-linenumber="2359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2347" class="line" lang="perl"><span class="idiff left right">    </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2359

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2359" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2348" 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">

2348

</td>

<td class="diff-line-num new_line" data-linenumber="2360" 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">

2360

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2360" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">n</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span> <span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2349" 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">

2349

</td>

<td class="diff-line-num new_line" data-linenumber="2361" 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">

2361

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2361" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2350" 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">

2350

</td>

<td class="diff-line-num new_line" data-linenumber="2362" 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">

2362

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2362" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;">==-</span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2372" 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">@@ -2360,7 +2372,7 @@ sub read_details {</td>

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<td class="diff-line-num old_line" data-linenumber="2360" 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">

2360

</td>

<td class="diff-line-num new_line" data-linenumber="2372" 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">

2372

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<pre style="margin: 0;"> <span id="LC2372" class="line" lang="perl">      <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Well then, proceeding...</span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2361" 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">

2361

</td>

<td class="diff-line-num new_line" data-linenumber="2373" 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">

2373

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<pre style="margin: 0;"> <span id="LC2373" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">goto</span> <span class="nv" style="color: #008080;">RESTART</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2362" 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">

2362

</td>

<td class="diff-line-num new_line" data-linenumber="2374" 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">

2374

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2374" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2363

</td>

<td class="diff-line-num new_line old" data-linenumber="2375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2363" class="line" lang="perl"><span class="idiff left right">      </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2375

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2375" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2364" 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">

2364

</td>

<td class="diff-line-num new_line" data-linenumber="2376" 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">

2376

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2376" class="line" lang="perl">      <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">The algorithm (-p=</span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;">) does not support the given input files (use --force to skip this behaviour)...</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2365" 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">

2365

</td>

<td class="diff-line-num new_line" data-linenumber="2377" 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">

2377

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2377" class="line" lang="perl"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2366" 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">

2366

</td>

<td class="diff-line-num new_line" data-linenumber="2378" 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">

2378

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2378" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: #008080;">$allowedAlphabet</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">a</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$cur_gene_is_valid</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">1</span> <span class="p">){</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2382" 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">@@ -2370,7 +2382,7 @@ sub read_details {</td>

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<td class="diff-line-num old_line" data-linenumber="2370" 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">

2370

</td>

<td class="diff-line-num new_line" data-linenumber="2382" 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">

2382

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<pre style="margin: 0;"> <span id="LC2382" class="line" lang="perl">      <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2371" 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">

2371

</td>

<td class="diff-line-num new_line" data-linenumber="2383" 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">

2383

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2383" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> [WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Found forbidden non-aminoacid character in input fasta file '</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">' in gene '</span><span class="si" style="color: #d14;">$lastgenename</span><span class="s2" style="color: #d14;">'. </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> expects aminoacid characters</span><span class="si" style="color: #d14;">$NC</span><span class="p">");</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2372" 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">

2372

</td>

<td class="diff-line-num new_line" data-linenumber="2384" 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">

2384

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2384" class="line" lang="perl">      <span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="2373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2373

</td>

<td class="diff-line-num new_line old" data-linenumber="2385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2373" class="line" lang="perl"><span class="idiff left right">    </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2385

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2385" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2374" 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">

2374

</td>

<td class="diff-line-num new_line" data-linenumber="2386" 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">

2386

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<pre style="margin: 0;"> <span id="LC2386" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: #008080;">$blastmode_pendant</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$restart_counter</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span> <span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">2</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># only for step = 0 and step 1 you can do a rerun else the DB are missing</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2375" 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">

2375

</td>

<td class="diff-line-num new_line" data-linenumber="2387" 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">

2387

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2387" class="line" lang="perl">        <span class="nv" style="color: #008080;">$blastmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$blastmode_pendant</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$blastmode</span><span class="p">};</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2376" 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">

2376

</td>

<td class="diff-line-num new_line" data-linenumber="2388" 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">

2388

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2388" class="line" lang="perl">        <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">("</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">!!!</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">[WARNING]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> Switching now to </span><span class="si" style="color: #d14;">$blastmode</span><span class="s2" style="color: #d14;"> and restarting...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2434" 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">@@ -2422,12 +2434,11 @@ sub read_details {</td>

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<td class="diff-line-num old_line" data-linenumber="2422" 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">

2422

</td>

<td class="diff-line-num new_line" data-linenumber="2434" 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">

2434

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2434" class="line" lang="perl"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2423" 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">

2423

</td>

<td class="diff-line-num new_line" data-linenumber="2435" 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">

2435

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<pre style="margin: 0;"> <span id="LC2435" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">Error</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="2424" 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">

2424

</td>

<td class="diff-line-num new_line" data-linenumber="2436" 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">

2436

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2436" class="line" lang="perl">  <span class="nv" style="color: #008080;">$debug</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2425

</td>

<td class="diff-line-num new_line old" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2425" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2426

</td>

<td class="diff-line-num new_line old" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2426" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">get_parameter</span><span class="p">;</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2437

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2437" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"</span><span class="s2" style="color: #d14;">I need at least two files to compare something!</span><span class="p">"){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">get_parameter</span><span class="p">;}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2427" 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">

2427

</td>

<td class="diff-line-num new_line" data-linenumber="2438" 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">

2438

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2438" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2428" 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">

2428

</td>

<td class="diff-line-num new_line" data-linenumber="2439" 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">

2439

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2439" class="line" lang="perl">  <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="se" style="color: #d14;">\n\n</span><span class="si" style="color: #d14;">$RED</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">[Error]</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$ORANGE</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\n\n</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2429" 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">

2429

</td>

<td class="diff-line-num new_line" data-linenumber="2440" 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">

2440

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2440" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2430

</td>

<td class="diff-line-num new_line old" data-linenumber="2441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2430" class="line" lang="perl">  <span class="k" style="font-weight: 600;"><span class="idiff left">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">(If you cannot solve this error, please send a report to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="si" style="color: #d14;"><span class="idiff">@incoming</span></span><span class="s2" style="color: #d14;"><span class="idiff">.gitlab.com including the parameter-vector above or visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for more help. Further more all mails to lechner</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="si" style="color: #d14;"><span class="idiff">@staff</span></span><span class="s2" style="color: #d14;"><span class="idiff">.uni-marburg.de are welcome)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n\n</span></span><span class="p"><span class="idiff right">";</span></span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2441

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2441" class="line" lang="perl">  <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$_</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">ne</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">I need at least two files to compare something!</span></span><span class="p"><span class="idiff">"){</span></span><span class="k" style="font-weight: 600;"><span class="idiff">print</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">STDERR</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">(If you cannot solve this error, please send a report to incoming+paulklemm-phd-proteinortho-7278443-issue-</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="si" style="color: #d14;"><span class="idiff">@incoming</span></span><span class="s2" style="color: #d14;"><span class="idiff">.gitlab.com including the parameter-vector above or visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes for more help. Further more all mails to lechner</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">\</span></span><span class="si" style="color: #d14;"><span class="idiff">@staff</span></span><span class="s2" style="color: #d14;"><span class="idiff">.uni-marburg.de are welcome)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n\n\n</span></span><span class="p"><span class="idiff right">";}</span></span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2431" 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">

2431

</td>

<td class="diff-line-num new_line" data-linenumber="2442" 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">

2442

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2442" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2432" 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">

2432

</td>

<td class="diff-line-num new_line" data-linenumber="2443" 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">

2443

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2443" class="line" lang="perl">  <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">reset_locale</span><span class="p">();</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2433" 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">

2433

</td>

<td class="diff-line-num new_line" data-linenumber="2444" 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">

2444

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2444" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$keep</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$tmp_path</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/\/proteinortho_cache_[^\/]+\d*\/$/</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$step</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">1</span> <span class="p">){</span><span class="nb" style="color: #0086b3;">system</span><span class="p">("</span><span class="s2" style="color: #d14;">rm -r </span><span class="si" style="color: #d14;">$tmp_path</span><span class="s2" style="color: #d14;"> >/dev/null 2>&1</span><span class="p">");}</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2465" 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">@@ -2454,7 +2465,7 @@ sub gff4fasta {</td>

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<td class="diff-line-num old_line" data-linenumber="2454" 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">

2454

</td>

<td class="diff-line-num new_line" data-linenumber="2465" 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">

2465

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2465" class="line" lang="perl">  <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$gff</span><span class="p">;</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2455" 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">

2455

</td>

<td class="diff-line-num new_line" data-linenumber="2466" 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">

2466

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2466" class="line" lang="perl"><span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2456" 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">

2456

</td>

<td class="diff-line-num new_line" data-linenumber="2467" 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">

2467

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2467" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="2457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2457

</td>

<td class="diff-line-num new_line old" data-linenumber="2468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2457" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">get_po_path</span> <span class="p">{</span><span class="idiff left right"> </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2468

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2468" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">get_po_path</span> <span class="p">{</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2458" 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">

2458

</td>

<td class="diff-line-num new_line" data-linenumber="2469" 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">

2469

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2469" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@tmppath</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">fileparse</span><span class="p">(</span><span class="nv" style="color: #008080;">$0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># path to the C++-part of this program</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2459" 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">

2459

</td>

<td class="diff-line-num new_line" data-linenumber="2470" 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">

2470

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2470" class="line" lang="perl"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2460" 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">

2460

</td>

<td class="diff-line-num new_line" data-linenumber="2471" 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">

2471

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2471" class="line" lang="perl">  <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$uname</span><span class="o" style="font-weight: 600;">=</span><span class="p">`</span><span class="sb" style="color: #d14;">uname -s</span><span class="p">`;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2492" 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">@@ -2481,9 +2492,9 @@ sub get_po_path {</td>

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<td class="diff-line-num old_line" data-linenumber="2481" 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">

2481

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<td class="diff-line-num new_line" data-linenumber="2492" 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">

2492

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<pre style="margin: 0;"> <span id="LC2492" class="line" lang="perl">    <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">x</span> <span class="p">"</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">/proteinortho_clustering</span><span class="p">"){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2482" 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">

2482

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<td class="diff-line-num new_line" data-linenumber="2493" 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">

2493

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<pre style="margin: 0;"> <span id="LC2493" class="line" lang="perl">      <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="p">"</span><span class="si" style="color: #d14;">$binpath</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2483" 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">

2483

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<td class="diff-line-num new_line" data-linenumber="2494" 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">

2494

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<pre style="margin: 0;"> <span id="LC2494" class="line" lang="perl">      <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: #008080;">$debug</span><span class="p">){</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Detected </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2484

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<td class="diff-line-num new_line old" data-linenumber="2495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2484" class="line" lang="perl">    <span class="p">}</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="2495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2495

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2495" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2485" 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">

2485

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<td class="diff-line-num new_line" data-linenumber="2496" 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">

2496

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<pre style="margin: 0;"> <span id="LC2496" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2486

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<td class="diff-line-num new_line old" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2486" class="line" lang="perl"><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2497

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2497" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2487" 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">

2487

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<td class="diff-line-num new_line" data-linenumber="2498" 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">

2498

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<pre style="margin: 0;"> <span id="LC2498" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: #008080;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_clustering</span><span class="p">"){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2488" 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">

2488

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<td class="diff-line-num new_line" data-linenumber="2499" 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">

2499

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<pre style="margin: 0;"> <span id="LC2499" class="line" lang="perl">    <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_clustering in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;"> , /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2489" 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">

2489

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<td class="diff-line-num new_line" data-linenumber="2500" 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">

2500

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<pre style="margin: 0;"> <span id="LC2500" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2515" 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">@@ -2504,7 +2515,7 @@ sub get_po_path {</td>

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<td class="diff-line-num old_line" data-linenumber="2504" 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">

2504

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<td class="diff-line-num new_line" data-linenumber="2515" 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">

2515

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<pre style="margin: 0;"> <span id="LC2515" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;">#   &Error("cannot find proteinortho2tree.pl in $tmppath[1].\nPlease do one of the following:\n A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)\n B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64\n C. specify the path to the binaries with -binpath=...\n";</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2505" 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">

2505

</td>

<td class="diff-line-num new_line" data-linenumber="2516" 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">

2516

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<pre style="margin: 0;"> <span id="LC2516" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;">#   exit 0;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2506" 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">

2506

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<td class="diff-line-num new_line" data-linenumber="2517" 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">

2517

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2517" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># }</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="2507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2507

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<td class="diff-line-num new_line old" data-linenumber="2518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2507" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: #008080;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_ffadj_mcs.py</span><span class="p">"){</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2518" style="width: 35px; color: rgba(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="LC2518" class="line" lang="perl">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: #008080;">x</span> <span class="nv" style="color: #008080;">$tmppath</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">/proteinortho_ffadj_mcs.py</span><span class="p">"</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$synteny</span></span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2508" 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">

2508

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<td class="diff-line-num new_line" data-linenumber="2519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2519" class="line" lang="perl">    <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">Error</span><span class="p">("</span><span class="s2" style="color: #d14;">cannot find proteinortho_ffadj_mcs.py</span><span class="si" style="color: #d14;">$NC</span><span class="s2" style="color: #d14;"> in: the current directory '.', ./src/, ./src/BUILD/</span><span class="si" style="color: #d14;">$uname</span><span class="s2" style="color: #d14;">, /usr/bin, /usr/local/bin, -binpath=</span><span class="si" style="color: #d14;">$binpath</span><span class="s2" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">Please do one of the following:</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> A. recompile proteinortho (with 'make clean', 'make' and 'make install' or 'make install PREFIX=...') or consider a installation with conda/brew (see the README for more informations)</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> B. execute from within the downloaded directory, there are precompiled binaries for Linux_x86_64</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> C. specify the path to the binaries with -binpath=...</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2520" class="line" lang="perl">    <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2510" 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">

2510

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<td class="diff-line-num new_line" data-linenumber="2521" 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">

2521

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<pre style="margin: 0;"> <span id="LC2521" class="line" lang="perl">  <span class="p">}</span></span>

</pre>

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</table>

<br>

</li>

<li id="e52fa9f6246a270e3b0a6a888a797d22f02e2532">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/46b56795faef96c95bb86901b1e453561560c447...49bbba390194d4ec62008d2ef6dcf58ea36447af#e52fa9f6246a270e3b0a6a888a797d22f02e2532"><strong>src/proteinortho_ffadj_mcs.py</strong></a>

<hr>

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<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env python2.7</span></span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">python3</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" 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">

2

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<td class="diff-line-num new_line" data-linenumber="2" 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">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std<span class="idiff left">out</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stderr</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">exit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxint</span></span></span>

</pre>

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<td class="diff-line-num new old_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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<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">

3

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">std<span class="idiff left">err</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">exit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxsize</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">copy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deepcopy</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num 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">

5

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">bisect</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">bisect</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">izip</span><span class="p">,</span> <span class="n" style="color: #333;">product</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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<td class="diff-line-num new_line old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">basename</span><span class="p">,</span> <span class="n" style="color: #333;">dirname</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="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">

6

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">product</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">random</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">randint</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">math</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ceil</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">csv</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">log</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">ALPHA</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

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<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">DIRECTION_CRICK_STRAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'+'</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">DIRECTION_WATSON_STRAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

<td class="diff-line-num new_line" data-linenumber="13" 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">

13

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

</td>

<td class="diff-line-num new_line" data-linenumber="14" 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">

14

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BothStrands</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC18" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'+'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'-'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">BothStrands</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'+'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'-'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">BothStrands</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'+/-'</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">DIRECTION_BOTH_STRANDS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BothStrands</span><span class="p">()</span></span>

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">LOG_FILENAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'info.log'</span></span>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Run</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># public variables</span></span>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python">    <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">    <span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="32" 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">@@ -37,7 +32,7 @@ class Run:</td>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">direction</span></span>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startG1</span></span>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startG2</span></span>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startG1</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(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="LC35" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startG1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startG2</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="41" 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">@@ -46,13 +41,12 @@ class Run:</td>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">        <span class="n" style="color: #333;">adjTerm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python">            <span class="n" style="color: #333;">adjTerm</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python">                <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)])</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python">        <span class="n" style="color: #333;">edgeTerm</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">**</span><span class="mi" style="color: #099;">2</span>  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        edgeTerm = max(self.weight)**2</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(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="LC44" class="line" lang="python">                           <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)])</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="python">        <span class="n" style="color: #333;">edgeTerm</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">**</span><span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">w</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">alpha</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">adjTerm</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">alpha</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">edgeTerm</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extendRun</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">nextG1</span><span class="p">,</span> <span class="n" style="color: #333;">nextG2</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextG1</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextG2</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="p">)</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,212 +54,193 @@ class Run:</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextG1</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextG2</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">weight</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__len__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__str__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'G1:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s G2:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (</span><span class="si" style="color: #d14;">%.5</span><span class="s" style="color: #d14;">f)'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;">alpha</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'G1:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s G2:</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s-</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (</span><span class="si" style="color: #d14;">%.5</span><span class="s" style="color: #d14;">f)'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">                                                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">                                                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;">ALPHA</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="65" 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">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#class DummyRun(Run):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    def __init__(self, weights):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        self.weight = weights</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readDistsAndOrder</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">edgeThreshold</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readDistsAndOrder</span><span class="p">(</span><span class="n" style="color: #333;">dist_file</span><span class="p">,</span> <span class="n" style="color: #333;">edgeThreshold</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python">    <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python">    <span class="n" style="color: #333;">hasMultipleChromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python">    <span class="n" style="color: #333;">g1_chrom<span class="idiff left">osomes</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">dict</span></span><span class="p"><span class="idiff right">()</span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">g2_chromosomes</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">dict</span></span><span class="p"><span class="idiff right">()</span></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">chr1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">chr2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python">    <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">csv</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">reader</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delimiter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">):</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">hasMultipleChromosomes</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">    <span class="n" style="color: #333;">g1_chrom<span class="idiff left">_pos</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2_chrom_pos</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{},</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{}</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">chr1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chr2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'0'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'0'</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">    <span class="k" style="font-weight: 600;"><span class="idiff left">with</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">dist_file</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">    <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">    <span class="idiff left">        </span><span class="n" style="color: #333;"><span class="idiff">cells</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rstrip</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">        <span class="idiff left right">    </span><span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">hasMultipleChromosomes</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<td class="diff-line-num new_line" data-linenumber="78" 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">

78

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

88

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">chr1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

90

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">g1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

91

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">chr2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

92

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

93

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

94

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">edgeWeight</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

95

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

96

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC96" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">g1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

97

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">g2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

98

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

99

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<td class="diff-line-num new_line old" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">edgeWeight</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">line</span></span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">        <span class="idiff left right">    </span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">chr1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">chr2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">edgeWeight</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">        <span class="idiff left right">    </span><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">edgeWeight</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">cells</span></span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" 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">

100

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<td class="diff-line-num new_line" data-linenumber="91" 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">

91

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

101

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<td class="diff-line-num new_line old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">edgeWeight</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">edgeThreshold</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

102

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<td class="diff-line-num new_line old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python">        <span class="idiff left right">    </span><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">edgeWeight</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">edgeThreshold</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python">            <span class="idiff left right">    </span><span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" 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">

103

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<td class="diff-line-num new_line" data-linenumber="94" 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">

94

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

104

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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_chromosomes</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chr1</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

105

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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">g1_chromosome</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2_chromosomes</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">chr2</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

107

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<td class="diff-line-num new_line old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC107" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">g2_chromosome</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC95" class="line" lang="python">        <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chr1</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g1_chrom_pos</span></span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff right">g1_chrom_po</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC97" class="line" lang="python">        <span class="idiff left">    </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chr2</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g2_chrom_pos</span></span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff right">g2_chrom_po</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" 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">

108

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<td class="diff-line-num new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">g1_chromosome</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<td class="diff-line-num new_line old" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left right">g2_chromosome</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python">        <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff right">g1_chrom_po</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python">        <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff right">g2_chrom_po</span>s</span><span class="p">[</span><span class="n" style="color: #333;">chr2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" 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">

111

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<td class="diff-line-num new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python">        <span class="n" style="color: #333;">l0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chr1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

113

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<td class="diff-line-num new_line old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python">        <span class="n" style="color: #333;">l1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chr2</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python">        <span class="idiff left right">    </span><span class="n" style="color: #333;">l0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chr1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">        <span class="idiff left right">    </span><span class="n" style="color: #333;">l1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">chr2</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" 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">

114

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<td class="diff-line-num new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l0</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python">            <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">l0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># append mapping pos in mappedGenome and the weight of the corresponding edge</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">l0</span><span class="p">][</span><span class="n" style="color: #333;">l1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'1'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">DIRECTION_CRICK_STRAND</span> <span class="ow" style="font-weight: 600;">or</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

119

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python">                <span class="n" style="color: #333;">DIRECTION_WATSON_STRAND</span><span class="p">,</span> <span class="n" style="color: #333;">edgeWeight</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(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="LC106" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l0</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">                <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">l0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># append mapping pos in mappedGenome and the weight of the corresponding edge</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="python">            <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">l0</span><span class="p">][</span><span class="n" style="color: #333;">l1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'1'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'+'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="n" style="color: #333;">edgeWeight</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" 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">

120

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<td class="diff-line-num new_line" data-linenumber="110" 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">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" 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">

121

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<td class="diff-line-num new_line" data-linenumber="111" 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">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># construct genome order</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

122

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<td class="diff-line-num new_line old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python">    <span class="n" style="color: #333;">tel1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">establish_linear_genome_order</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">g1_chromosome</span>s</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

123

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<td class="diff-line-num new_line old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python">    <span class="n" style="color: #333;">tel2</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">establish_linear_genome_order</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">g2_chromosome</span>s</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python">    <span class="n" style="color: #333;">tel1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">sort_genome</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">g1_chrom_po</span>s</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python">    <span class="n" style="color: #333;">tel2</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">sort_genome</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">g2_chrom_po</span>s</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" 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">

124

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<td class="diff-line-num new_line" data-linenumber="114" 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">

114

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># add telomeres</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="116" 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">

116

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t1</span><span class="p">,</span> <span class="n" style="color: #333;">t2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">product</span><span class="p">(</span><span class="n" style="color: #333;">tel1</span><span class="p">,</span> <span class="n" style="color: #333;">tel2</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

127

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<td class="diff-line-num new_line old" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t1</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">t1</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">res</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" 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">

128

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<td class="diff-line-num new_line" data-linenumber="118" 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">

118

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python">            <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">t1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

129

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python">        <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">t1</span><span class="p">][</span><span class="n" style="color: #333;">t2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">DIRECTION_BOTH_STRANDS</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

131

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    res[maxint] = dict([</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

132

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (maxint, (DIRECTION_WATSON_STRAND, 1)), </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

133

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (0,      (DIRECTION_WATSON_STRAND, 1)), </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

134

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (maxint, (DIRECTION_CRICK_STRAND, 1)),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (0,      (DIRECTION_CRICK_STRAND, 1))])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

136

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    res[maxint] = dict([</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

137

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (maxint, (DIRECTION_WATSON_STRAND, 1)), </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

138

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (0,      (DIRECTION_WATSON_STRAND, 1)),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

139

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (maxint, (DIRECTION_CRICK_STRAND, 1)), </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#        (0,      (DIRECTION_CRICK_STRAND, 1))])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(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="LC119" class="line" lang="python">        <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">t1</span><span class="p">][</span><span class="n" style="color: #333;">t2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">BothStrands</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" 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">

141

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<td class="diff-line-num new_line" data-linenumber="120" 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">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="121" 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">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">res</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" 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">

143

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<td class="diff-line-num new_line" data-linenumber="122" 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">

122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">establish_linear_genome_order</span><span class="p">(</span><span class="n" style="color: #333;">chromosomes</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(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="LC123" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(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="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sort_genome</span><span class="p">(</span><span class="n" style="color: #333;">chrom_pos</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="145" 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">

145

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<td class="diff-line-num new_line" data-linenumber="125" 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">

125

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">    <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="146" 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">

146

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python">    <span class="n" style="color: #333;">telomeres</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">chrom<span class="idiff left right">osome</span>s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">chrom<span class="idiff left right">_po</span>s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">        <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">        <span class="n" style="color: #333;">telomeres</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python">        <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">([(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">chrom<span class="idiff left right">osome</span>s</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">])])</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python">        <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">max<span class="idiff left right">int</span></span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python">        <span class="n" style="color: #333;">telomeres</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">max<span class="idiff left right">int</span></span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(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="LC130" class="line" lang="python">        <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">([(</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">chrom<span class="idiff left right">_po</span>s</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">])])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(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="LC131" class="line" lang="python">        <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">max<span class="idiff left right">size</span></span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(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="LC132" class="line" lang="python">        <span class="n" style="color: #333;">telomeres</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">((</span><span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">max<span class="idiff left right">size</span></span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">telomeres</span><span class="p">,</span> <span class="n" style="color: #333;">g</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(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="LC134" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python">    <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">runList</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python">    <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ALPHA</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">runList</span></span><span class="p"><span class="idiff right">]</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="157" 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">

157

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<td class="diff-line-num new_line" data-linenumber="138" 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">

138

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">run</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runs</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

158

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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python">        <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

159

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<td class="diff-line-num new_line old" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python">        <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python">        <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bisect</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python">        <span class="n" style="color: #333;">keys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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<td class="diff-line-num new_line" data-linenumber="141" 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">

141

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">        <span class="n" style="color: #333;">runList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" 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">

161

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<td class="diff-line-num new_line" data-linenumber="142" 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">

142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">checkMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">dist</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" 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">

165

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<td class="diff-line-num new_line" data-linenumber="143" 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">

143

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(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="LC144" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">checkMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">dist</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(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="LC145" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(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="LC146" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" 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">

166

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<td class="diff-line-num new_line" data-linenumber="147" 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">

147

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="167" 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">

167

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<td class="diff-line-num new_line" data-linenumber="148" 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">

148

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'G1 and G2 have unequal length: len(G1) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, len(G2)'</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

169

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<td class="diff-line-num new_line old" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python">                <span class="s" style="color: #d14;">' </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(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="LC149" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'unequal length: |G1| = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d, |G2| = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="170" 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">

170

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<td class="diff-line-num new_line" data-linenumber="150" 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">

150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

171

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<td class="diff-line-num new_line old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC171" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Annotation vector length doesn</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">t match with genome '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

172

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<td class="diff-line-num new_line old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python">                <span class="s" style="color: #d14;">'length: len(G1) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, len(g1_runs) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, len(G2) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, len('</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC173" class="line" lang="python">                <span class="s" style="color: #d14;">'g2_runs) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

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<td class="diff-line-num new_line old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC174" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">)))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Annotation vector length does not match with genome '</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(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="LC152" class="line" lang="python">                   <span class="s" style="color: #d14;">'length: len(G1) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, len(g1_runs) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, len(G2) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, len('</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="python">                   <span class="s" style="color: #d14;">'g2_runs) = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" 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">

175

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<td class="diff-line-num new_line" data-linenumber="154" 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">

154

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" 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">

176

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<td class="diff-line-num new_line" data-linenumber="155" 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">

155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">    <span class="n" style="color: #333;">all_included</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

177

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<td class="diff-line-num new_line old" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python">    <span class="n" style="color: #333;">r_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python">    <span class="n" style="color: #333;">r_counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="178" 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">

178

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<td class="diff-line-num new_line" data-linenumber="157" 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">

157

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">    <span class="n" style="color: #333;">prev_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" 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">

179

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python">    <span class="n" style="color: #333;">c_adj</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

180

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<td class="diff-line-num new_line old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_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">

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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="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="181" 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">

181

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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

182

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is not included in any run'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is not included in any run'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="183" 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">

183

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<td class="diff-line-num new_line" data-linenumber="162" 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">

162

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" 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">

184

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<td class="diff-line-num new_line" data-linenumber="163" 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">

163

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC163" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

185

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC185" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is included in more than one run: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff right"> </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

186

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<td class="diff-line-num new_line old" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC186" class="line" lang="python">                <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

164

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is included in more than one run: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">],</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="python">                <span class="idiff left right">      </span><span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" 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">

187

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<td class="diff-line-num new_line" data-linenumber="166" 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">

166

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

188

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<td class="diff-line-num new_line old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"><span class="idiff left right">       </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

167

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" 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">

189

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python">        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="190" 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">

190

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<td class="diff-line-num new_line" data-linenumber="169" 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">

169

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="170" 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">

170

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev_run</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="192" 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">

192

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<td class="diff-line-num new_line" data-linenumber="171" 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">

171

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python">            <span class="n" style="color: #333;">c_adj</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="172" 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">

172

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runs</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<td class="diff-line-num new_line old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s not included in run list.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

173

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s not included in run list.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" 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">

195

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<td class="diff-line-num new_line" data-linenumber="174" 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">

174

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_included</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

196

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<td class="diff-line-num new_line old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC196" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s occurs twice in G1. Current gene '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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<td class="diff-line-num new_line old" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC197" class="line" lang="python">                        <span class="s" style="color: #d14;">'position: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

175

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s occurs twice in G1. Current gene position: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

</pre>

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198

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<td class="diff-line-num new_line" data-linenumber="176" 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">

176

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python">            <span class="n" style="color: #333;">r_counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python">            <span class="n" style="color: #333;">prev_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

177

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python">            <span class="n" style="color: #333;">prev_run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="200" 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">

200

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<td class="diff-line-num new_line" data-linenumber="178" 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">

178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="201" 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">

201

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<td class="diff-line-num new_line" data-linenumber="179" 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">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">        <span class="n" style="color: #333;">all_included</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="202" 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">

202

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<td class="diff-line-num new_line" data-linenumber="180" 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">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">        <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="182" 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">

182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python">            <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="183" 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">

183

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="184" 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">

184

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python">            <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">k</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="207" 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">

207

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<td class="diff-line-num new_line" data-linenumber="185" 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">

185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python">        <span class="n" style="color: #333;">eWgt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dist</span><span class="p">[</span><span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]][</span><span class="n" style="color: #333;">g2j</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="186" 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">

186

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="209" 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">

209

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<td class="diff-line-num new_line" data-linenumber="187" 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">

187

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">eWgt</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC210" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Edge weight of </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s-</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s differs in run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s, should be'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python">                <span class="s" style="color: #d14;"><span class="idiff left">' </span></span><span class="si" style="color: #d14;"><span class="idiff">%.6</span></span><span class="s" style="color: #d14;"><span class="idiff">f but is </span></span><span class="si" style="color: #d14;"><span class="idiff">%.6</span></span><span class="s" style="color: #d14;"><span class="idiff">f'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">g2j</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">eWgt</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(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="LC188" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Edge weight of </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s-</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s differs in run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s, should be </span></span><span class="si" style="color: #d14;"><span class="idiff">%.6</span></span><span class="s" style="color: #d14;"><span class="idiff">f but is </span></span><span class="si" style="color: #d14;"><span class="idiff">%.6</span></span><span class="s" style="color: #d14;"><span class="idiff">f'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python">                <span class="idiff left right">      </span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">g2j</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">eWgt</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python">    <span class="n" style="color: #333;">missing_runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_included</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">symmetric_difference</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">missing_runs</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Additional runs in runslist that are not part in the'</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python">                <span class="s" style="color: #d14;">' matching: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">missing_runs</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python">        </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Number of adjacencies is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s in matching of size </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">c_adj</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python">        <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">   </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(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="LC193" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Additional runs in runslist that are not part in the matching: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(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="LC194" class="line" lang="python">                  <span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">missing_runs</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(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="LC195" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

196

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Number of adjacencies is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s in matching of size </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">c_adj</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

197

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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="221" 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">

221

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<td class="diff-line-num new_line" data-linenumber="198" 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">

198

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r_counter</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

222

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<td class="diff-line-num new_line old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python">        <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Sum of run lengths does not equal matching size! Sum '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

223

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<td class="diff-line-num new_line old" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python">                <span class="s" style="color: #d14;">'of run lengths: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, matching size: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">r_counter</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

199

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Sum of run lengths does not equal matching size! Sum '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

200

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python">                <span class="idiff left right">   </span><span class="s" style="color: #d14;">'of run lengths: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, matching size: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">r_counter</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="224" 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">

224

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<td class="diff-line-num new_line" data-linenumber="201" 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">

201

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

225

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<td class="diff-line-num new_line old" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

202

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="226" 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">

226

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<td class="diff-line-num new_line" data-linenumber="203" 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">

203

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

227

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<td class="diff-line-num new_line old" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC227" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is not included in any run'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(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="LC204" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is not included in any run'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="205" 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">

205

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

229

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<td class="diff-line-num new_line old" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is included in more than one run: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff right"> </span></span>

</pre>

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230

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python">                <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(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="LC206" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Gene </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s is included in more than one run: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff right">],</span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python">                <span class="idiff left right">      </span><span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))))</span></span>

</pre>

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231

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<td class="diff-line-num new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">difference</span><span class="p">(</span><span class="n" style="color: #333;">all_included</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'G2 differs in runs from G1 on position </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff right"> </span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python">                <span class="s" style="color: #d14;"><span class="idiff left">', '</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff right">,</span></span><span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">difference</span><span class="p">(</span><span class="n" style="color: #333;">all_included</span><span class="p">)))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'G2 differs in runs from G1 on position </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff right">],</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python">                <span class="idiff left">      </span><span class="s" style="color: #d14;"><span class="idiff">', '</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">difference</span><span class="p">(</span><span class="n" style="color: #333;">all_included</span><span class="p">)))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="212" 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">

212

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runs</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1pos</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1pos</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> \</span>

</pre>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python">                <span class="n" style="color: #333;">g2pos</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2pos</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python">            <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Positions of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s can not be mapped back to the'</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<td class="diff-line-num new_line old" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python">                    <span class="s" style="color: #d14;">' genomes.'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="215" style="width: 35px; color: rgba(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="LC215" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Positions of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s can not be mapped back to the genomes.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> \</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python">                <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python">            <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Positions of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s exceed borders of the '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python">                    <span class="s" style="color: #d14;">'genomes'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(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="LC219" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Positions of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s exceed borders of the genomes'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">!=</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python">                <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left right">ging</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Start of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is not coherent with genome '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(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="LC223" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Start of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is not coherent with genome '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python">                    <span class="s" style="color: #d14;">'position on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (G1) or </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (G2)'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]],</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python">                        <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]]))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left right">ging</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'End of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is not coherent with genome '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(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="LC227" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'End of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is not coherent with genome '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">                    <span class="s" style="color: #d14;">'position on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (G1) or </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (G2)'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python">                        <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]]))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python">                <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left right">ging</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Length of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is erroneous: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (on G1), </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num new old_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">

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<td class="diff-line-num new new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Length of run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is erroneous: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s (on G1), </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python">                    <span class="s" style="color: #d14;">'(on G2)'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python">                        <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]))</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left right">ging</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Number of weights does not comply with run length. '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Number of weights does not comply with run length. '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python">                    <span class="s" style="color: #d14;">'Weights: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, run length: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, run: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python">                        <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">))</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python">                        <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python">        <span class="n" style="color: #333;">g1_chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g1pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG1</span></span><span class="p"><span class="idiff">]:</span></span><span class="n" style="color: #333;"><span class="idiff">g1pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">])</span>)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python">        <span class="n" style="color: #333;">g2_chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG2</span></span><span class="p"><span class="idiff">]:</span></span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG2</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">])</span>)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python">        <span class="n" style="color: #333;">g1_chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(<span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g1pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG1</span></span><span class="p"><span class="idiff">]:</span></span><span class="n" style="color: #333;"><span class="idiff">g1pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]]</span>)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python">        <span class="n" style="color: #333;">g2_chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(<span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG2</span></span><span class="p"><span class="idiff">]:</span></span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG2</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]]</span>)</span></span>

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<td class="diff-line-num new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_chromosomes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_chromosomes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

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<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left right">ging</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Number of chromosomes on G1 (#chrs: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s) or G2 '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<td class="diff-line-num new old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">((</span><span class="s" style="color: #d14;">'Number of chromosomes on G1 (#chrs: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s) or G2 '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python">                    <span class="s" style="color: #d14;">'(#chrs: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s) in run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is not 1 (Meaning that possibly'</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python">                    <span class="s" style="color: #d14;">' the run extends over two or more chromosomes, which '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<td class="diff-line-num new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">                    <span class="s" style="color: #d14;">'shouldn</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">t be allowed).'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_chromosomes</span><span class="p">),</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="248" 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">@@ -273,15 +248,15 @@ def checkMatching(g1, g2, g1_runs, g2_runs, runs, dist):</td>

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># are all runs merged that can be merged?</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python">    <span class="n" style="color: #333;">run_ends</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runs</span><span class="p">:</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runs</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python">            <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python">            <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python">            <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">            <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python">        <span class="n" style="color: #333;">g1i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python">        <span class="n" style="color: #333;">g1i2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">run_ends</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">g1i2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">run_ends</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="264" 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">@@ -289,134 +264,131 @@ def checkMatching(g1, g2, g1_runs, g2_runs, runs, dist):</td>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">            <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python">            <span class="n" style="color: #333;">g2i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">            <span class="n" style="color: #333;">g2i2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_ends</span><span class="p">[</span><span class="n" style="color: #333;">g1i2</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">g2i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">g2i2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Runs </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s could be merged, but are not!'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">])[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">])[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]))</span></span><span class="idiff right"> </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

294

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<td class="diff-line-num new_line old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left">elif</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DIRECTION_WATSON_STRAND</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2i2</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

295

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<td class="diff-line-num new_line old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">logging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Runs </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s could be merged, but are not!'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">])[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">])[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]))</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

296

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<td class="diff-line-num new_line old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

297

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<td class="diff-line-num new_line old" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"><span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">getAllRuns</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff right">):</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

267

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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">g2i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">g2i2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

268

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Runs </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s could be merged, but are not!'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

269

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC269" class="line" lang="python">            <span class="idiff left">              </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]))[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]))[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]))</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

270

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left">elif</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'-'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2i2</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

271

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"> <span class="idiff left">               </span><span class="n" style="color: #333;"><span class="idiff">log</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Runs </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s could be merged, but are not!'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"><span class="idiff left">                          </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]))[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]))[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]))</span></span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getAllRuns</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python">    <span class="n" style="color: #333;">g1_runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">set</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python">    <span class="n" style="color: #333;">g2_runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">set</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">    <span class="n" style="color: #333;">activeRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python">    <span class="n" style="color: #333;">reportedRuns</span><span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python">    <span class="n" style="color: #333;">reportedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python">        <span class="n" style="color: #333;">curPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> </span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python">        </span>

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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)):</span></span>

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<td class="diff-line-num new old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python">        <span class="n" style="color: #333;">curPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

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<td class="diff-line-num new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python">        <span class="n" style="color: #333;">newRunList</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">        <span class="n" style="color: #333;">forbiddenRunStarts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># check if link exists, otherwise terminate all runs</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python">        <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">curPos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span></span>

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<td class="diff-line-num old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># iterate over all runs</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">activeRuns</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python">            <span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python">            <span class="n" style="color: #333;">jEnd</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python">            <span class="n" style="color: #333;">jStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">curPos</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># run could not be extended </span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">((</span><span class="s" style="color: #d14;">'Terminate and report run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, because </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is on a'</span> <span class="o" style="font-weight: 600;">+</span> \</span>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python">                        <span class="s" style="color: #d14;">' different chromosome.'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">curPos</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># run could not be extended</span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'terminating run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, continue with </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">curPos</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python">                <span class="n" style="color: #333;">reportedRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># extend to the right</span></span>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">DIRECTION_CRICK_STRAND</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jEnd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span> \</span>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python">                <span class="ow" style="font-weight: 600;"><span class="idiff left right">and</span></span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">][</span><span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python">                <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left">'+'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jEnd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">and</span></span> \</span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python">                <span class="idiff left right">   </span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">][</span><span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python">                <span class="idiff left">    </span><span class="s" style="color: #d14;"><span class="idiff right">'+'</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">                <span class="n" style="color: #333;">g2_gene_r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python">                <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extendRun</span><span class="p">(</span><span class="n" style="color: #333;">curPos</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene_r</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">][</span><span class="n" style="color: #333;">g2_gene_r</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="333" 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">

333

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<td class="diff-line-num new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python">                <span class="n" style="color: #333;">newRunList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

334

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<td class="diff-line-num new_line old" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python">                <span class="n" style="color: #333;">forbiddenRunStarts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene_r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python">                <span class="n" style="color: #333;">forbiddenRunStarts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene_r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python">                <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python">                <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">jEnd</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Extended run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s to the right'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Extended run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s to the right'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># extend to the left</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_WATSON_STRAND</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">jStart</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> \</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'-'</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">jStart</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python">                    <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jStart</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">][</span><span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jStart</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> \</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python">                    <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_WATSON_STRAND</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jStart</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python">                    <span class="s" style="color: #d14;"><span class="idiff left right">'-'</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jStart</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python">                <span class="n" style="color: #333;">g2_gene_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">jStart</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">                <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extendRun</span><span class="p">(</span><span class="n" style="color: #333;">curPos</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene_l</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">curPos</span><span class="p">][</span><span class="n" style="color: #333;">g2_gene_l</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python">                <span class="n" style="color: #333;">newRunList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python">                <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python">                <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">jStart</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python">                <span class="n" style="color: #333;">forbiddenRunStarts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_WATSON_STRAND</span></span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene_l</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Extended run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s to the left'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python">                <span class="n" style="color: #333;">forbiddenRunStarts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="s" style="color: #d14;"><span class="idiff left right">'-'</span></span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene_l</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Extended run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s to the left'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># run could not be extended<span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left right">ging</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">((</span><span class="s" style="color: #d14;">'Terminate and report run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, because </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s has '</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python">                    <span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'no further consecutive edge.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">curPos</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># run could not be extended</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="323" style="width: 35px; color: rgba(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="LC323" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">((</span><span class="s" style="color: #d14;">'Terminate and report run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, because </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s has '</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

324

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python">                    <span class="idiff left">      </span><span class="s" style="color: #d14;"><span class="idiff">'no further consecutive edge.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">curPos</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="354" 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">

354

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<td class="diff-line-num new_line" data-linenumber="325" 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">

325

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python">                <span class="n" style="color: #333;">reportedRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="356" 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">

356

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<td class="diff-line-num new_line" data-linenumber="327" 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">

327

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if no edge exists, nothing has to be done...</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="357" 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">

357

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<td class="diff-line-num new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">g2_gene</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">d</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">curPos</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">(</span>):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">g2_gene</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">curPos</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">()</span>):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="359" 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">

359

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<td class="diff-line-num new_line" data-linenumber="330" 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">

330

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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">forbiddenRunStarts</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

360

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<td class="diff-line-num new_line old" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python">                    <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">g2_gene</span><span class="p">]</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

331

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python">                    <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">g2_gene</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="361" 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">

361

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<td class="diff-line-num new_line" data-linenumber="332" 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">

332

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">BothStrands</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

362

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<td class="diff-line-num new_line old" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC362" class="line" lang="python">                        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Run</span><span class="p">(</span><span class="n" style="color: #333;">curPos</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

333

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python">                        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Run</span><span class="p">(</span><span class="n" style="color: #333;">curPos</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="363" 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">

363

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<td class="diff-line-num new_line" data-linenumber="334" 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">

334

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python">                        <span class="n" style="color: #333;">newRunList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="364" 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">

364

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<td class="diff-line-num new_line" data-linenumber="335" 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">

335

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python">                        <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python">                        <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python">                        <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Start new (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s) run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python">                        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Run</span><span class="p">(</span><span class="n" style="color: #333;">curPos</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_WATSON_STRAND</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="337" style="width: 35px; color: rgba(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="LC337" class="line" lang="python">                        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Start new (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s) run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="338" style="width: 35px; color: rgba(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="LC338" class="line" lang="python">                        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Run</span><span class="p">(</span><span class="n" style="color: #333;">curPos</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left right">'-'</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python">                        <span class="n" style="color: #333;">newRunList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python">                        <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python">                        <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python">                        <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Start new (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s) run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="342" style="width: 35px; color: rgba(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="LC342" class="line" lang="python">                        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Start new (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s) run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python">                        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Run</span><span class="p">(</span><span class="n" style="color: #333;">curPos</span><span class="p">,</span> <span class="n" style="color: #333;">g2_gene</span><span class="p">,</span> <span class="n" style="color: #333;">weight</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python">                        <span class="n" style="color: #333;">newRunList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">                        <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python">                        <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python">                        <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Start new (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s) run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="348" style="width: 35px; color: rgba(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="LC348" class="line" lang="python">                        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">debug</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Start new (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s) run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python">        <span class="n" style="color: #333;">activeRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRunList</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python">    <span class="n" style="color: #333;">reportedRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">activeRuns</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">reportedRuns</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="353" style="width: 35px; color: rgba(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="LC353" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">replaceByNew</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">r_old</span><span class="p">,</span> <span class="n" style="color: #333;">r_new</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python">    <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">r_old</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python">        <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r_old</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python">        <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python">        <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r_old</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC359" class="line" lang="python">        <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python">        <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+=</span></span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python">        <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+=</span></span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="360" style="width: 35px; color: rgba(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="LC360" class="line" lang="python">        <span class="n" style="color: #333;">i</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

361

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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python">        <span class="n" style="color: #333;">j</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="390" 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">

390

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<td class="diff-line-num new_line" data-linenumber="362" 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">

362

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">j</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="391" 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">

391

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<td class="diff-line-num new_line" data-linenumber="363" 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">

363

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="392" 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">

392

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<td class="diff-line-num new_line" data-linenumber="364" 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">

364

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="366" 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">

366

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">doMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

395

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<td class="diff-line-num new_line old" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="367" style="width: 35px; color: rgba(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="LC367" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="368" style="width: 35px; color: rgba(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="LC368" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="397" 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">

397

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<td class="diff-line-num new_line" data-linenumber="369" 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">

369

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python">    <span class="n" style="color: #333;">newRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="370" 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">

370

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC371" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="400" 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">

400

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<td class="diff-line-num new_line" data-linenumber="372" 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">

372

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC372" class="line" lang="python">        <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="401" 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">

401

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<td class="diff-line-num new_line" data-linenumber="373" 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">

373

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">        <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">k</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="402" 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">

402

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<td class="diff-line-num new_line" data-linenumber="374" 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">

374

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="403" 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">

403

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<td class="diff-line-num new_line" data-linenumber="375" 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">

375

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC375" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="404" 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">

404

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<td class="diff-line-num new_line" data-linenumber="376" 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">

376

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC376" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

405

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<td class="diff-line-num new_line old" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC405" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

377

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC377" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="406" 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">

406

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<td class="diff-line-num new_line" data-linenumber="378" 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">

378

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC378" class="line" lang="python">            <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="407" 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">

407

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<td class="diff-line-num new_line" data-linenumber="379" 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">

379

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="408" 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">

408

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<td class="diff-line-num new_line" data-linenumber="380" 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">

380

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="409" 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">

409

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<td class="diff-line-num new_line" data-linenumber="381" 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">

381

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC381" class="line" lang="python">                <span class="n" style="color: #333;">runList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

410

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<td class="diff-line-num new_line old" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

382

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="411" 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">

411

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<td class="diff-line-num new_line" data-linenumber="383" 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">

383

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="412" 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">

412

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<td class="diff-line-num new_line" data-linenumber="384" 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">

384

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">                <span class="n" style="color: #333;">overlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

413

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<td class="diff-line-num new_line old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC413" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s overlaps with selected run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s by </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

414

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<td class="diff-line-num new_line old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC414" class="line" lang="python">                        <span class="s" style="color: #d14;"><span class="idiff left">'at position G1:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s overlaps with selected run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s by </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

386

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python">                        <span class="idiff left">  </span><span class="s" style="color: #d14;"><span class="idiff">'at position G1:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

</pre>

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415

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<td class="diff-line-num new_line" data-linenumber="387" 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">

387

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python">                <span class="n" style="color: #333;">r_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="416" 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">

416

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<td class="diff-line-num new_line" data-linenumber="388" 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">

388

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python">                <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<td class="diff-line-num old old_line" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

417

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<td class="diff-line-num new_line old" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="389" style="width: 35px; color: rgba(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="LC389" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="418" 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">

418

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<td class="diff-line-num new_line" data-linenumber="390" 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">

390

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># check weight</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

419

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<td class="diff-line-num new_line old" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">overlap</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(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="LC391" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">overlap</span> <span class="o" style="font-weight: 600;">-</span><span class="idiff left right"> </span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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420

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<td class="diff-line-num new_line" data-linenumber="392" 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">

392

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="400" 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">@@ -428,29 +400,29 @@ def doMatching(g1, g2, g1_runs, g2_runs, m, runList):</td>

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<td class="diff-line-num new_line" data-linenumber="400" 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">

400

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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">overlap</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python">                    <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="402" 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">

402

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python">                <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

431

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<td class="diff-line-num new_line old" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Divided overlapping run in </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

403

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Divided overlapping run in </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="432" 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">

432

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<td class="diff-line-num new_line" data-linenumber="404" 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">

404

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># do you see that r.startG2 is already at the right position?</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="405" 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">

405

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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python">                <span class="n" style="color: #333;">replaceByNew</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

434

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<td class="diff-line-num new_line old" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python">                        <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

406

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python">                        <span class="idiff left right">     </span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="435" 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">

435

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<td class="diff-line-num new_line" data-linenumber="407" 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">

407

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python">                <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

436

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<td class="diff-line-num new_line old" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

408

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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="437" 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">

437

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<td class="diff-line-num new_line" data-linenumber="409" 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">

409

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">i</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

438

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<td class="diff-line-num new_line old" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

410

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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="439" 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">

439

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<td class="diff-line-num new_line" data-linenumber="411" 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">

411

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python">                    <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="440" 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">

440

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<td class="diff-line-num new_line" data-linenumber="412" 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">

412

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python">                    <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># run start cannot be larger than i</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s interfers with current run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s at '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python">                        <span class="s" style="color: #d14;"><span class="idiff left">'position G1:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Shifting.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s interfers with current run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s at '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python">                        <span class="idiff left">  </span><span class="s" style="color: #d14;"><span class="idiff">'position G1:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Shifting.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python">                <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC448" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="449" style="width: 35px; color: rgba(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="LC420" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"></span>

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453

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<td class="diff-line-num new_line old" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC453" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Shifted run is now located at </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

425

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Shifted run is now located at </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python">                <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">newRuns</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python">                <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="431" 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">@@ -459,99 +431,93 @@ def doMatching(g1, g2, g1_runs, g2_runs, m, runList):</td>

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<td class="diff-line-num new_line" data-linenumber="431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">m</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="diff-line-num old_line" data-linenumber="461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python">            <span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC462" class="line" lang="python"><span class="idiff left right"> </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="436" 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">

436

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python">                <span class="n" style="color: #333;">runList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC465" class="line" lang="python"><span class="idiff left right">            </span></span>

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<td class="diff-line-num new old_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="437" style="width: 35px; color: rgba(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="LC437" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">j</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python">                <span class="n" style="color: #333;">overlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s overlaps with selected run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s by </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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469

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<td class="diff-line-num new_line old" data-linenumber="440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python">                        <span class="s" style="color: #d14;"><span class="idiff left">'at position G2:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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440

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s overlaps with selected run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s by </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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441

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python">                        <span class="idiff left">  </span><span class="s" style="color: #d14;"><span class="idiff">'at position G2:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))</span></span>

</pre>

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442

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python">                <span class="n" style="color: #333;">r_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">deepcopy</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="471" 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">

471

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<td class="diff-line-num new_line" data-linenumber="443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python">                <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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472

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<td class="diff-line-num new_line old" data-linenumber="444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="idiff left right"> </span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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444

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

445

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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474

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<td class="diff-line-num new_line" data-linenumber="446" 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">

446

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="447" 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">

447

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="476" 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">

476

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<td class="diff-line-num new_line" data-linenumber="448" 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">

448

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">overlap</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python">                    <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="451" style="width: 35px; color: rgba(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="LC451" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python">                    <span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[:</span><span class="n" style="color: #333;">overlap</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">overlap</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python">                    <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="456" 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">

456

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python">                <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC485" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Divided overlapping run in </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s and </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                # do you see that r.startG1 is already at the right position?</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                if r.direction == DIRECTION_CRICK_STRAND:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC488" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                    g1_runs[g1pos[r.endG1]].remove(r)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                else:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="457" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC490" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#                    g1_runs[g1pos[r.startG1]].remove(r)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Divided overlapping run in </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s and </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="491" 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">

491

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<td class="diff-line-num new_line" data-linenumber="458" 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">

458

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python">                <span class="n" style="color: #333;">replaceByNew</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

492

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<td class="diff-line-num new_line old" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python">                        <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python">                        <span class="idiff left right">     </span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="493" 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">

493

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<td class="diff-line-num new_line" data-linenumber="460" 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">

460

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python">                <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r_new</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="461" 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">

461

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="495" 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">

495

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<td class="diff-line-num new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">j</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

496

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<td class="diff-line-num new_line old" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="464" 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">

464

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python">                    <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="465" 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">

465

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="466" 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">

466

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC466" class="line" lang="python">                    <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="467" 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">

467

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC467" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="501" 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">

501

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<td class="diff-line-num new_line" data-linenumber="468" 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">

468

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="502" 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">

502

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<td class="diff-line-num new_line" data-linenumber="469" 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">

469

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># run start cannot be larger than j</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

503

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<td class="diff-line-num new_line old" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC503" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s interfers with current run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s at '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

504

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<td class="diff-line-num new_line old" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python">                        <span class="s" style="color: #d14;"><span class="idiff left">'position G2:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Shifting.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

470

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s interfers with current run </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s at '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

471

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python">                        <span class="idiff left">  </span><span class="s" style="color: #d14;"><span class="idiff">'position G2:</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Shifting.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="505" 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">

505

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<td class="diff-line-num new_line" data-linenumber="472" 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">

472

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python">                <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

506

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<td class="diff-line-num new_line old" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

473

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC473" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="507" 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">

507

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<td class="diff-line-num new_line" data-linenumber="474" 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">

474

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC474" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="508" 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">

508

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<td class="diff-line-num new_line" data-linenumber="475" 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">

475

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC475" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="509" 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">

509

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<td class="diff-line-num new_line" data-linenumber="476" 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">

476

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC476" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="510" 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">

510

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<td class="diff-line-num new_line" data-linenumber="477" 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">

477

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC477" class="line" lang="python">                    <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="511" 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">

511

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<td class="diff-line-num new_line" data-linenumber="478" 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">

478

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC478" class="line" lang="python">                    <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

512

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<td class="diff-line-num new_line old" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC512" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Shifted run is now located at </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

479

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC479" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Shifted run is now located at </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="513" 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">

513

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<td class="diff-line-num new_line" data-linenumber="480" 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">

480

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC480" class="line" lang="python">                <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="514" 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">

514

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<td class="diff-line-num new_line" data-linenumber="481" 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">

481

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC481" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">newRuns</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python">                <span class="n" style="color: #333;">newRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="483" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python">    <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mergeRuns</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">,</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="488" style="width: 35px; color: rgba(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="LC488" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="521" 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">

521

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<td class="diff-line-num new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python">    <span class="n" style="color: #333;">newRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python">    <span class="n" style="color: #333;">wSrt</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;">alpha</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python">    <span class="n" style="color: #333;">mod_g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

525

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<td class="diff-line-num new_line old" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="493" 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">

493

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python">        <span class="n" style="color: #333;">g1i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mod_g1</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span></span>

</pre>

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527

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<td class="diff-line-num new_line" data-linenumber="494" 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">

494

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python">        <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="528" 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">

528

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<td class="diff-line-num new_line" data-linenumber="495" 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">

495

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

529

</td>

<td class="diff-line-num new_line" data-linenumber="496" 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">

496

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC496" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="530" 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">

530

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<td class="diff-line-num new_line" data-linenumber="497" 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">

497

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC497" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

531

</td>

<td class="diff-line-num new_line old" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="532" 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">

532

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<td class="diff-line-num new_line" data-linenumber="498" 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">

498

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># To understand this piece of code, one observation is important:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

533

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<td class="diff-line-num new_line old" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If r1 or r2 is already matched, then there exist only one combination</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If r1 or r2 is already matched, then there exist<span class="idiff left right">s</span> only one combination</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="534" 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">

534

</td>

<td class="diff-line-num new_line" data-linenumber="500" 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">

500

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># of possible merges. If r1 and r2 are both unmatched, several merges</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

535

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<td class="diff-line-num new_line old" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># are possible and all should be done.<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># are possible and all should be done.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="536" 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">

536

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<td class="diff-line-num new_line" data-linenumber="502" 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">

502

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># After each merge between a matched and unmatched run, the newly</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="537" 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">

537

</td>

<td class="diff-line-num new_line" data-linenumber="503" 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">

503

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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># merged run must be completely matched, before further modification</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

538

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<td class="diff-line-num new_line old" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC538" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># points (mod_g1) can be processed.<span class="idiff left right"> </span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

504

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC504" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># points (mod_g1) can be processed.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="539" 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">

539

</td>

<td class="diff-line-num new_line" data-linenumber="505" 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">

505

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="540" 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">

540

</td>

<td class="diff-line-num new_line" data-linenumber="506" 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">

506

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC506" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">product</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">difference</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

541

</td>

<td class="diff-line-num new_line old" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">wSrt</span></span><span class="p">,</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

542

</td>

<td class="diff-line-num new_line old" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC542" class="line" lang="python">                <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">difference</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">wSrt</span></span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

543

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<td class="diff-line-num new_line old" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC543" class="line" lang="python">                    <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

507

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python">            <span class="idiff left">                         </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ALPHA</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

508

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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python">                <span class="idiff left">              </span><span class="nb" style="color: #0086b3;"><span class="idiff">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">difference</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">])</span>,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

509

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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python">                    <span class="idiff left">                 </span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ALPHA</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="544" 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">

544

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<td class="diff-line-num new_line" data-linenumber="510" 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">

510

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="545" 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">

545

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<td class="diff-line-num new_line" data-linenumber="511" 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">

511

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python">                    <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="ow" style="font-weight: 600;">and</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="546" 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">

546

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<td class="diff-line-num new_line" data-linenumber="512" 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">

512

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python">                    <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="547" 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">

547

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<td class="diff-line-num new_line" data-linenumber="513" 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">

513

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python">                    <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

548

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<td class="diff-line-num new_line old" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python">                    <span class="p">((</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left">DIRECTION_CRICK_STRAND</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

549

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<td class="diff-line-num new_line old" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python">                    <span class="n" style="color: #333;"><span class="idiff left">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

550

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<td class="diff-line-num new_line old" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python">                    <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DIRECTION_WATSON_STRAND</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

551

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<td class="diff-line-num new_line old" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC551" class="line" lang="python">                    <span class="n" style="color: #333;"><span class="idiff left">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">-</span></span><span class="mi" style="color: #099;">1</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

514

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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python">                    <span class="p">((</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left">'+'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">and</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

515

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python">                    <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">or</span></span></span>

</pre>

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516

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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python">                    <span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'-'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff right">and</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

517

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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python">                    <span class="idiff left">  </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">endG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2pos</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">r1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">startG2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">)):</span></span>

</pre>

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552

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<td class="diff-line-num new_line" data-linenumber="518" 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">

518

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"></span>

</pre>

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553

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<td class="diff-line-num new_line old" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Merge runs </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">))</span></span>

</pre>

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554

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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span><span class="p">:</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Merge runs </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s and </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

520

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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span><span class="p">:</span></span>

</pre>

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555

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<td class="diff-line-num new_line" data-linenumber="521" 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">

521

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python">                    <span class="n" style="color: #333;">runList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="522" 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">

522

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">runList</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="523" 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">

523

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC523" class="line" lang="python">                    <span class="n" style="color: #333;">runList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="527" 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">@@ -561,13 +527,13 @@ def mergeRuns(mod_g1, g1, g2, g1_runs, g2_runs, runList, alreadyMatched):</td>

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527

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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="562" 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">

562

</td>

<td class="diff-line-num new_line" data-linenumber="528" 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">

528

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python">                <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="563" 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">

563

</td>

<td class="diff-line-num new_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

529

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python">                <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

564

</td>

<td class="diff-line-num new_line old" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC564" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

530

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<pre style="margin: 0;">+<span id="LC530" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="565" 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">

565

</td>

<td class="diff-line-num new_line" data-linenumber="531" 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">

531

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python">                    <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="566" 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">

566

</td>

<td class="diff-line-num new_line" data-linenumber="532" 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">

532

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<pre style="margin: 0;"> <span id="LC532" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="567" 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">

567

</td>

<td class="diff-line-num new_line" data-linenumber="533" 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">

533

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python">                    <span class="n" style="color: #333;">r2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

568

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<td class="diff-line-num new_line old" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC568" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Merged run is </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

534

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC534" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Merged run is </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">r2</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="569" 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">

569

</td>

<td class="diff-line-num new_line" data-linenumber="535" 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">

535

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">                <span class="n" style="color: #333;">replaceByNew</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

570

</td>

<td class="diff-line-num new_line old" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC570" class="line" lang="python">                        <span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">],</span> <span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

536

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC536" class="line" lang="python">                        <span class="idiff left right">     </span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">r1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">],</span> <span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="571" 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">

571

</td>

<td class="diff-line-num new_line" data-linenumber="537" 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">

537

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC537" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r2</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p">)</span> <span class="o" style="font-weight: 600;">^</span> <span class="p">(</span><span class="n" style="color: #333;">r1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p">):</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="572" 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">

572

</td>

<td class="diff-line-num new_line" data-linenumber="538" 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">

538

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC538" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alreadyMatched</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="573" 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">

573

</td>

<td class="diff-line-num new_line" data-linenumber="539" 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">

539

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC539" class="line" lang="python">                        <span class="n" style="color: #333;">alreadyMatched</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="551" 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">@@ -585,6 +551,7 @@ def mergeRuns(mod_g1, g1, g2, g1_runs, g2_runs, runList, alreadyMatched):</td>

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<td class="diff-line-num old_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python">    <span class="n" style="color: #333;">insertIntoRunList</span><span class="p">(</span><span class="n" style="color: #333;">newRuns</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="553" 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">

553

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="554" style="width: 35px; color: rgba(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="LC554" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="588" 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">

588

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<td class="diff-line-num new_line" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">removeSingleGenes</span><span class="p">(</span><span class="n" style="color: #333;">genome</span><span class="p">,</span> <span class="n" style="color: #333;">genome_runs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python">    <span class="n" style="color: #333;">del_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">    <span class="n" style="color: #333;">mod_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="563" 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">@@ -596,37 +563,39 @@ def removeSingleGenes(genome, genome_runs):</td>

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<td class="diff-line-num old_line" data-linenumber="596" 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">

596

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<td class="diff-line-num new_line" data-linenumber="563" 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">

563

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="python">            <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">genome</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="597" 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">

597

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<td class="diff-line-num new_line" data-linenumber="564" 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">

564

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python">            <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">genome_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

599

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<td class="diff-line-num new_line old" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC599" class="line" lang="python">            <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><span class="idiff left right">+=</span></span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

566

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<pre style="margin: 0;">+<span id="LC566" class="line" lang="python">            <span class="n" style="color: #333;">i</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="600" 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">

600

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<td class="diff-line-num new_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">del_res</span><span class="p">,</span> <span class="n" style="color: #333;">mod_res</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="601" 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">

601

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<td class="diff-line-num new_line" data-linenumber="568" 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">

568

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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

569

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC569" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="602" 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">

602

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<td class="diff-line-num new_line" data-linenumber="570" 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">

570

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="603" 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">

603

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<td class="diff-line-num new_line" data-linenumber="571" 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">

571

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python">    <span class="n" style="color: #333;">g2dists</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g1i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">dists</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">(</span>):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

605

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<td class="diff-line-num new_line old" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC605" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g2j</span><span class="p">,</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">(</span>):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

572

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<pre style="margin: 0;">+<span id="LC572" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g1i</span><span class="p">,</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">dists</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">()</span>):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

573

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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g2j</span><span class="p">,</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">()</span>):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="606" 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">

606

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<td class="diff-line-num new_line" data-linenumber="574" 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">

574

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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g2j</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2dists</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="607" 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">

607

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<td class="diff-line-num new_line" data-linenumber="575" 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">

575

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python">                <span class="n" style="color: #333;">g2dists</span><span class="p">[</span><span class="n" style="color: #333;">g2j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="608" 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">

608

</td>

<td class="diff-line-num new_line" data-linenumber="576" 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">

576

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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python">            <span class="n" style="color: #333;">g2dists</span><span class="p">[</span><span class="n" style="color: #333;">g2j</span><span class="p">][</span><span class="n" style="color: #333;">g1i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="609" 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">

609

</td>

<td class="diff-line-num new_line" data-linenumber="577" 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">

577

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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="610" 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">

610

</td>

<td class="diff-line-num new_line" data-linenumber="578" 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">

578

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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># copy g1, g2 and dists map, because we'll modify it. Also remove all genes</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="611" 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">

611

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<td class="diff-line-num new_line" data-linenumber="579" 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">

579

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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># that do not contain edges.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

612

</td>

<td class="diff-line-num new_line old" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python">    <span class="n" style="color: #333;">g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">dists</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff right">)</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">dists</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">])]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

613

</td>

<td class="diff-line-num new_line old" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC613" class="line" lang="python">    <span class="n" style="color: #333;">g2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">g2dists</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff right">)</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2dists</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">])]</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

580

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC580" class="line" lang="python">    <span class="n" style="color: #333;">g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">dists</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">dists</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">])]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

581

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC581" class="line" lang="python">    <span class="n" style="color: #333;">g2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g2dists</span></span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2dists</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">])]</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="614" 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">

614

</td>

<td class="diff-line-num new_line" data-linenumber="582" 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">

582

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

615

</td>

<td class="diff-line-num new_line old" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC615" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

583

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC583" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="616" 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">

616

</td>

<td class="diff-line-num new_line" data-linenumber="584" 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">

584

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC584" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="617" 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">

617

</td>

<td class="diff-line-num new_line" data-linenumber="585" 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">

585

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC585" class="line" lang="python">    <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getAllRuns</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

618

</td>

<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC618" class="line" lang="python">    <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Found </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s runs.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

619

</td>

<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC619" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># sort<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

620

</td>

<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC620" class="line" lang="python">    <span class="n" style="color: #333;">runList</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">alpha</span></span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

621

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<td class="diff-line-num new_line old" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC621" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

586

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC586" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Found </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s runs.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

587

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC587" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># sort</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

588

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC588" class="line" lang="python">    <span class="n" style="color: #333;">runList</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">runs</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ALPHA</span></span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="622" 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">

622

</td>

<td class="diff-line-num new_line" data-linenumber="590" 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">

590

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC590" class="line" lang="python">    <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="623" 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">

623

</td>

<td class="diff-line-num new_line" data-linenumber="591" 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">

591

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC591" class="line" lang="python">    <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">runList</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

624

</td>

<td class="diff-line-num new_line old" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC624" class="line" lang="python">        <span class="n" style="color: #333;">noOfAdjacencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">filter</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">runList</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

592

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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python">        <span class="n" style="color: #333;">noOfAdjacencies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(<span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">runList</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ALPHA</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getWeight</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ALPHA</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span></span>

</pre>

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625

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<td class="diff-line-num new_line" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC593" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">noOfAdjacencies</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python">            <span class="n" style="color: #333;">randPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">noOfAdjacencies</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="627" 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">

627

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<td class="diff-line-num new_line" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="596" 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">

596

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<pre style="margin: 0;"> <span id="LC596" class="line" lang="python">            <span class="n" style="color: #333;">randPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">randint</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runList</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC629" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'From </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, select randomly among top </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runList</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ceil</span><span class="p">((</span><span class="n" style="color: #333;">noOfAdjacencies</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runList</span><span class="p">))</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">)),</span> <span class="n" style="color: #333;">runList</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">randPos</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

597

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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'From </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, select randomly among top </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s run </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

598

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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python">                 <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runList</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ceil</span><span class="p">((</span><span class="n" style="color: #333;">noOfAdjacencies</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">runList</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">)),</span> <span class="n" style="color: #333;">runList</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">randPos</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="599" 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">

599

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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python">        <span class="n" style="color: #333;">mx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runList</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">randPos</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="600" 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">

600

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<pre style="margin: 0;"> <span id="LC600" class="line" lang="python">        <span class="n" style="color: #333;">mod_g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC601" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">mx</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="603" 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">@@ -634,46 +603,46 @@ def findRandomRunSequence(g1, g2, dists, topXperCent):</td>

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># update run list</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="635" 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">

635

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<td class="diff-line-num new_line" data-linenumber="604" 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">

604

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python">            <span class="n" style="color: #333;">doMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">mx</span><span class="p">,</span> <span class="n" style="color: #333;">runList</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="636" 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">

636

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<td class="diff-line-num new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python">            <span class="n" style="color: #333;">del_g1</span><span class="p">,</span> <span class="n" style="color: #333;">new_mod_g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeSingleGenes</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">)</span></span>

</pre>

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637

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<td class="diff-line-num new_line old" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC637" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">del_g1</span><span class="p">:</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

638

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<td class="diff-line-num new_line old" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC638" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Zombie genes removed from G1: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">del_g1</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC606" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">del_g1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

607

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC607" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Zombie genes removed from G1: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">del_g1</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="639" 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">

639

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<td class="diff-line-num new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># it can happen that a gene in mod_g1 has already been deleted</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="640" 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">

640

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<td class="diff-line-num new_line" data-linenumber="609" 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">

609

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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># before being processed. This happens if there is a merge between</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="641" 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">

641

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<td class="diff-line-num new_line" data-linenumber="610" 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">

610

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<pre style="margin: 0;"> <span id="LC610" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># a matched and unmatched run. Then some genes remain unprocessed</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="642" 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">

642

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<td class="diff-line-num new_line" data-linenumber="611" 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">

611

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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># while the merged run is re-matched. In this process, new genes</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="643" 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">

643

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<td class="diff-line-num new_line" data-linenumber="612" 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">

612

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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># can be deleted. If one of the genes happens to be in mod_g1, it</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

644

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<td class="diff-line-num new_line old" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC644" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># should be deleted.<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

613

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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># should be deleted.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="645" 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">

645

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<td class="diff-line-num new_line" data-linenumber="614" 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">

614

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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">del_g1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">intersection</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="646" 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">

646

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<td class="diff-line-num new_line" data-linenumber="615" 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">

615

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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python">                    <span class="n" style="color: #333;">mod_g1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="647" 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">

647

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<td class="diff-line-num new_line" data-linenumber="616" 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">

616

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC616" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

648

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<td class="diff-line-num new_line old" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC648" class="line" lang="python">                <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="649" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

617

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<pre style="margin: 0;">+<span id="LC617" class="line" lang="python">                <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="649" 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">

649

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<td class="diff-line-num new_line" data-linenumber="618" 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">

618

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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># add new modification points</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="650" 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">

650

</td>

<td class="diff-line-num new_line" data-linenumber="619" 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">

619

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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python">            <span class="n" style="color: #333;">mod_g1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">new_mod_g1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="651" 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">

651

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<td class="diff-line-num new_line" data-linenumber="620" 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">

620

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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="652" 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">

652

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<td class="diff-line-num new_line" data-linenumber="621" 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">

621

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python">            <span class="n" style="color: #333;">del_g2</span><span class="p">,</span> <span class="n" style="color: #333;">mod_g2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeSingleGenes</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="653" 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">

653

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<td class="diff-line-num new_line" data-linenumber="622" 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">

622

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC622" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">del_g2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

654

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<td class="diff-line-num new_line old" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC654" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Zombie genes removed from G2: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">del_g2</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

623

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC623" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Zombie genes removed from G2: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">del_g2</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="655" 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">

655

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<td class="diff-line-num new_line" data-linenumber="624" 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">

624

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g2j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mod_g2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

656

</td>

<td class="diff-line-num new_line old" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC656" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g1i</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">g2dists</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2j</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">(</span>):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

625

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC625" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g1i</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2dists</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">g2j</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">items</span></span><span class="p"><span class="idiff right">()</span>):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="657" 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">

657

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<td class="diff-line-num new_line" data-linenumber="626" 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">

626

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC626" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

658

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<td class="diff-line-num new_line old" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC658" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

627

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC627" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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659

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<td class="diff-line-num new_line" data-linenumber="628" 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">

628

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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python">                                <span class="n" style="color: #333;">mod_g1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">g1i</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

660

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<td class="diff-line-num new_line old" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">what, if d == DIRECTION_BOTH_STRANDS? Then,</span> both neighbors have to be added...</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

661

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<td class="diff-line-num new_line old" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC661" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_WATSON_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

629

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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">d == DIRECTION_BOTH_STRANDS?</span> both neighbors have to be added...</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

630

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'-'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="662" 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">

662

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<td class="diff-line-num new_line" data-linenumber="631" 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">

631

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python">                                <span class="n" style="color: #333;">mod_g1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="663" 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">

663

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<td class="diff-line-num new_line" data-linenumber="632" 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">

632

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># merge runs</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="664" 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">

664

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<td class="diff-line-num new_line" data-linenumber="633" 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">

633

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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python">            <span class="n" style="color: #333;">mx</span><span class="p">,</span> <span class="n" style="color: #333;">mod_g1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mergeRuns</span><span class="p">(</span><span class="n" style="color: #333;">mod_g1</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span></span>

</pre>

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665

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<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python">                    <span class="n" style="color: #333;">runList</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

666

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<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC666" class="line" lang="python">  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

667

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<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC667" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">:</span> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

668

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<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC668" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Matching finished. Longest run size is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

669

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<td class="diff-line-num new_line old" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="python">            <span class="n" style="color: #333;">res</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

634

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC634" class="line" lang="python">                                   <span class="n" style="color: #333;">runList</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

635

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC635" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

636

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC636" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">res</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

637

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC637" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Matching finished. Longest run size is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">)))))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python">        <span class="n" style="color: #333;">log<span class="idiff left right">ging</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Matching finished, but no runs found. Empty input?'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="639" style="width: 35px; color: rgba(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="LC639" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Matching finished, but no runs found. Empty input?'</span><span class="p">)</span></span>

</pre>

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672

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<td class="diff-line-num new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">res</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="642" 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">

642

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="643" style="width: 35px; color: rgba(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="LC643" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">repeatMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">repMatching</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="676" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python">        <span class="n" style="color: #333;">minCsSize</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="645" style="width: 35px; color: rgba(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="LC645" class="line" lang="python">        <span class="idiff left right">           </span><span class="n" style="color: #333;">minCsSize</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python">    <span class="n" style="color: #333;">g1_mod_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_mod</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python">    <span class="n" style="color: #333;">g2_mod_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2_mod</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="650" 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">@@ -681,24 +650,23 @@ def repeatMatching(g1, g2, g1_mod, g2_mod, g1_runs, g2_runs, dists, repMatching,</td>

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<td class="diff-line-num old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python">    <span class="n" style="color: #333;">g2_runs_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2_runs</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python">    <span class="n" style="color: #333;">selectedRuns_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC684" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="685" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

686

</td>

<td class="diff-line-num new_line old" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC686" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

653

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

654

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC654" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="687" 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">

687

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<td class="diff-line-num new_line" data-linenumber="655" 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">

655

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC655" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="688" 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">

688

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<td class="diff-line-num new_line" data-linenumber="656" 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">

656

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python">    <span class="n" style="color: #333;">noReps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repMatching</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="689" 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">

689

</td>

<td class="diff-line-num new_line" data-linenumber="657" 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">

657

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC657" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="690" 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">

690

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<td class="diff-line-num new_line" data-linenumber="658" 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">

658

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python">    <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">repMatching</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

691

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<td class="diff-line-num new_line old" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC691" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

659

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="692" 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">

692

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<td class="diff-line-num new_line" data-linenumber="660" 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">

660

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC660" class="line" lang="python">            <span class="n" style="color: #333;">run_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="693" 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">

693

</td>

<td class="diff-line-num new_line" data-linenumber="661" 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">

661

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC661" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">run_set</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

694

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC694" class="line" lang="python">                <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Expected run, set length of 1, but was told'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="695" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

695

</td>

<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC695" class="line" lang="python">                        <span class="s" style="color: #d14;"><span class="idiff left">' different: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">', '</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">run_set</span></span><span class="p"><span class="idiff right">)</span>)))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

696

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<td class="diff-line-num new_line old" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC696" class="line" lang="python">            <span class="n" style="color: #333;">run</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">run_set</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">next</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="662" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

662

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC662" class="line" lang="python">                <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">error</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Expected run, set length of 1, but was told different: </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

663

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python">                        <span class="idiff left">  </span><span class="s" style="color: #d14;"><span class="idiff">', '</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">run_set</span></span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="664" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

664

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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python">            <span class="n" style="color: #333;">run</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">next</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">run_set</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff right">())</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="697" 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">

697

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<td class="diff-line-num new_line" data-linenumber="665" 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">

665

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="698" 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">

698

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<td class="diff-line-num new_line" data-linenumber="666" 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">

666

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python">            <span class="n" style="color: #333;">g1i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_mod</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="699" 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">

699

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<td class="diff-line-num new_line" data-linenumber="667" 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">

667

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="700" 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">

700

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<td class="diff-line-num new_line" data-linenumber="668" 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">

668

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="python">            <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

701

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<td class="diff-line-num new_line old" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC701" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;"><span class="idiff left right">DIRECTION_CRICK_STRAND</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

669

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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;"><span class="idiff left right">'+'</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="702" 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">

702

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<td class="diff-line-num new_line" data-linenumber="670" 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">

670

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python">                <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="703" 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">

703

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<td class="diff-line-num new_line" data-linenumber="671" 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">

671

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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="672" 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">

672

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="python">                <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="676" 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">@@ -708,190 +676,160 @@ def repeatMatching(g1, g2, g1_mod, g2_mod, g1_runs, g2_runs, dists, repMatching,</td>

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<td class="diff-line-num old_line" data-linenumber="708" 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">

708

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<td class="diff-line-num new_line" data-linenumber="676" 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">

676

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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python">                <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">dists</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="709" 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">

709

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<td class="diff-line-num new_line" data-linenumber="677" 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">

677

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="710" 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">

710

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<td class="diff-line-num new_line" data-linenumber="678" 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">

678

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC678" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">dists</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

711

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<td class="diff-line-num new_line old" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC711" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'Removed all edges in the input graph. Stopping '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

712

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<td class="diff-line-num new_line old" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC712" class="line" lang="python">                    <span class="s" style="color: #d14;"><span class="idiff left">'iteration </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span> <span class="p">(</span><span class="n" style="color: #333;">noReps</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

679

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'Removed all edges in the input graph. Stopping iteration </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

680

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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python">                     <span class="p">(</span><span class="n" style="color: #333;">noReps</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="713" 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">

713

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<td class="diff-line-num new_line" data-linenumber="681" 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">

681

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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="714" 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">

714

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<td class="diff-line-num new_line" data-linenumber="682" 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">

682

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="715" 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">

715

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<td class="diff-line-num new_line" data-linenumber="683" 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">

683

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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python">        <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">topXperCent</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="716" 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">

716

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<td class="diff-line-num new_line" data-linenumber="684" 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">

684

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<pre style="margin: 0;"> <span id="LC684" class="line" lang="python">        <span class="n" style="color: #333;">checkMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="717" 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">

717

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<td class="diff-line-num new_line" data-linenumber="685" 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">

685

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

718

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<td class="diff-line-num new_line old" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC718" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">((</span><span class="s" style="color: #d14;">'Obtained </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s adjacencies in matching of size </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s from '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

719

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<td class="diff-line-num new_line old" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC719" class="line" lang="python">                <span class="s" style="color: #d14;">'iteration </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

720

</td>

<td class="diff-line-num new_line old" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC720" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">),</span> <span class="n" style="color: #333;">noReps</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

686

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC686" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Obtained </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s adjacencies in matching of size </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s from iteration </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.'</span> <span class="o" style="font-weight: 600;">%</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

687

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python">                 <span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">),</span> <span class="n" style="color: #333;">noReps</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="721" 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">

721

</td>

<td class="diff-line-num new_line" data-linenumber="688" 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">

688

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC688" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="722" 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">

722

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<td class="diff-line-num new_line" data-linenumber="689" 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">

689

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<pre style="margin: 0;"> <span id="LC689" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># remove runs that fall below min length of minCsSize</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

723

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<td class="diff-line-num new_line old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC723" class="line" lang="python">        <span class="n" style="color: #333;">ff</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">next</span></span><span class="p"><span class="idiff right">(</span>))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minCsSize</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

724

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<td class="diff-line-num new_line old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC724" class="line" lang="python">        <span class="n" style="color: #333;">g1_mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">g1_mod</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">))</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ff</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

725

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<td class="diff-line-num new_line old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC725" class="line" lang="python">        <span class="n" style="color: #333;">g2_mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">g2_mod</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">))</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ff</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

726

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<td class="diff-line-num new_line old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC726" class="line" lang="python">        <span class="n" style="color: #333;">g1_runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">filter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g1_runs</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

727

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<td class="diff-line-num new_line old" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC727" class="line" lang="python">        <span class="n" style="color: #333;">g2_runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">filter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g2_runs</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

690

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python">        <span class="n" style="color: #333;">ff</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">next</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">__iter__</span></span><span class="p"><span class="idiff right">()</span>))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minCsSize</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

691

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python">        <span class="n" style="color: #333;">g1_mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">g1_mod</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">))</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ff</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])]</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

692

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python">        <span class="n" style="color: #333;">g2_mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">g2_mod</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">))</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ff</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])]</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

693

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python">        <span class="n" style="color: #333;">g1_runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g1_runs</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

694

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python">        <span class="n" style="color: #333;">g2_runs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">filter</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">g2_runs</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="728" 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">

728

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<td class="diff-line-num new_line" data-linenumber="695" 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">

695

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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python">        <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">s</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">minCsSize</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="729" 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">

729

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<td class="diff-line-num new_line" data-linenumber="696" 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">

696

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="730" 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">

730

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<td class="diff-line-num new_line" data-linenumber="697" 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">

697

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># stop if no runs were found matching the criteria</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="731" 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">

731

</td>

<td class="diff-line-num new_line" data-linenumber="698" 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">

698

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC698" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">):</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

732

</td>

<td class="diff-line-num new_line old" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC732" class="line" lang="python">            <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">((</span></span><span class="s" style="color: #d14;"><span class="idiff">'No feasible runs found in matching round </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Stopping '</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff right"> \</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

733

</td>

<td class="diff-line-num new_line old" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC733" class="line" lang="python">                    <span class="s" style="color: #d14;"><span class="idiff left">'iteration.'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span> <span class="p">(</span><span class="n" style="color: #333;">noReps</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC699" class="line" lang="python">            <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'No feasible runs found in matching round </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s. Stopping iteration.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

700

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC700" class="line" lang="python">                     <span class="p">(</span><span class="n" style="color: #333;">noReps</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="734" 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">

734

</td>

<td class="diff-line-num new_line" data-linenumber="701" 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">

701

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC701" class="line" lang="python">            <span class="k" style="font-weight: 600;">break</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="735" 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">

735

</td>

<td class="diff-line-num new_line" data-linenumber="702" 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">

702

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC702" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

736

</td>

<td class="diff-line-num new_line old" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC736" class="line" lang="python">        <span class="n" style="color: #333;">log<span class="idiff left">ging</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s feasible runs retained.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">%</span></span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

703

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC703" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s feasible runs retained.'</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="737" 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">

737

</td>

<td class="diff-line-num new_line" data-linenumber="704" 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">

704

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC704" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="738" 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">

738

</td>

<td class="diff-line-num new_line" data-linenumber="705" 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">

705

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC705" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># reconciliate with result data</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

739

</td>

<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC739" class="line" lang="python">        <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">))))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

740

</td>

<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC740" class="line" lang="python">        <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">))))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

741

</td>

<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC741" class="line" lang="python">        <span class="n" style="color: #333;">g2pos_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod_res</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod_res</span><span class="p">))))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

742

</td>

<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC742" class="line" lang="python">        <span class="n" style="color: #333;">g1pos_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod_res</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod_res</span><span class="p">))))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

743

</td>

<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC743" class="line" lang="python">        </span>

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<td class="diff-line-num old old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC744" class="line" lang="python">        <span class="n" style="color: #333;">chr_srt</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<td class="diff-line-num old old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC745" class="line" lang="python">        <span class="n" style="color: #333;">g1_mod_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod_res</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g1_mod</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">cmp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chr_srt</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC746" class="line" lang="python">        <span class="n" style="color: #333;">g2_mod_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod_res</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">cmp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chr_srt</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="706" style="width: 35px; color: rgba(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="LC706" class="line" lang="python">        <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="707" style="width: 35px; color: rgba(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="LC707" class="line" lang="python">        <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="708" style="width: 35px; color: rgba(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="LC708" class="line" lang="python">        <span class="n" style="color: #333;">g2pos_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod_res</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod_res</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

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<pre style="margin: 0;">+<span id="LC709" class="line" lang="python">        <span class="n" style="color: #333;">g1pos_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod_res</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod_res</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="python">        <span class="n" style="color: #333;">g1_mod_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod_res</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g1_mod</span><span class="p">),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

712

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<pre style="margin: 0;">+<span id="LC712" class="line" lang="python">        <span class="n" style="color: #333;">g2_mod_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">g2_mod_res</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="747" 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">

747

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<td class="diff-line-num new_line" data-linenumber="713" 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">

713

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python">        <span class="n" style="color: #333;">g1_runs_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="748" 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">

748

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<td class="diff-line-num new_line" data-linenumber="714" 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">

714

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python">        <span class="n" style="color: #333;">g2_runs_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>

</pre>

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749

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<td class="diff-line-num new_line" data-linenumber="715" 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">

715

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="750" 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">

750

</td>

<td class="diff-line-num new_line" data-linenumber="716" 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">

716

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC716" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g1i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g1_mod_new</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="751" 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">

751

</td>

<td class="diff-line-num new_line" data-linenumber="717" 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">

717

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC717" class="line" lang="python">            <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

752

</td>

<td class="diff-line-num new_line old" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC752" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1<span class="idiff left">pos_res</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1i</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC718" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1<span class="idiff left">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g1pos_res</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="753" 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">

753

</td>

<td class="diff-line-num new_line" data-linenumber="719" 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">

719

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC719" class="line" lang="python">                <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs_res</span><span class="p">[</span><span class="n" style="color: #333;">g1pos_res</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

754

</td>

<td class="diff-line-num new_line old" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC754" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1<span class="idiff left">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g1i</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC720" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g1<span class="idiff left">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g1pos</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="755" 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">

755

</td>

<td class="diff-line-num new_line" data-linenumber="721" 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">

721

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC721" class="line" lang="python">                <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">g1pos</span><span class="p">[</span><span class="n" style="color: #333;">g1i</span><span class="p">]])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="756" 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">

756

</td>

<td class="diff-line-num new_line" data-linenumber="722" 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">

722

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC722" class="line" lang="python">            <span class="n" style="color: #333;">g1_runs_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="757" 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">

757

</td>

<td class="diff-line-num new_line" data-linenumber="723" 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">

723

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="758" 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">

758

</td>

<td class="diff-line-num new_line" data-linenumber="724" 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">

724

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC724" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">g2j</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g2_mod_new</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="759" 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">

759

</td>

<td class="diff-line-num new_line" data-linenumber="725" 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">

725

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC725" class="line" lang="python">            <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

760

</td>

<td class="diff-line-num new_line old" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC760" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g2<span class="idiff left">pos_res</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2j</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC726" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g2<span class="idiff left">j</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g2pos_res</span></span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="761" 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">

761

</td>

<td class="diff-line-num new_line" data-linenumber="727" 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">

727

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC727" class="line" lang="python">                <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs_res</span><span class="p">[</span><span class="n" style="color: #333;">g2pos_res</span><span class="p">[</span><span class="n" style="color: #333;">g2j</span><span class="p">]])</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

762

</td>

<td class="diff-line-num new_line old" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC762" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g2<span class="idiff left">pos</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">g2j</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC728" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">g2<span class="idiff left">j</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">g2pos</span></span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="763" 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">

763

</td>

<td class="diff-line-num new_line" data-linenumber="729" 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">

729

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC729" class="line" lang="python">                <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">g2_runs</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">g2j</span><span class="p">]])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

764

</td>

<td class="diff-line-num new_line old" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC764" class="line" lang="python">            <span class="n" style="color: #333;">g2_runs_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC730" class="line" lang="python">            <span class="n" style="color: #333;">g2_runs_new</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="765" 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">

765

</td>

<td class="diff-line-num new_line" data-linenumber="731" 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">

731

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC731" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="766" 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">

766

</td>

<td class="diff-line-num new_line" data-linenumber="732" 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">

732

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC732" class="line" lang="python">        <span class="n" style="color: #333;">g1_mod_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_mod_new</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="767" 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">

767

</td>

<td class="diff-line-num new_line" data-linenumber="733" 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">

733

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC733" class="line" lang="python">        <span class="n" style="color: #333;">g2_mod_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2_mod_new</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="768" 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">

768

</td>

<td class="diff-line-num new_line" data-linenumber="734" 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">

734

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC734" class="line" lang="python">        <span class="n" style="color: #333;">g1_runs_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_runs_new</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="769" 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">

769

</td>

<td class="diff-line-num new_line" data-linenumber="735" 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">

735

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC735" class="line" lang="python">        <span class="n" style="color: #333;">g2_runs_res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2_runs_new</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="770" 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">

770

</td>

<td class="diff-line-num new_line" data-linenumber="736" 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">

736

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC736" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

771

</td>

<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC771" class="line" lang="python">        <span class="n" style="color: #333;">selectedRuns_res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

737

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC737" class="line" lang="python">        <span class="n" style="color: #333;">selectedRuns_res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="772" 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">

772

</td>

<td class="diff-line-num new_line" data-linenumber="738" 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">

738

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC738" class="line" lang="python">        <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="773" 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">

773

</td>

<td class="diff-line-num new_line" data-linenumber="739" 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">

739

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC739" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="774" 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">

774

</td>

<td class="diff-line-num new_line" data-linenumber="740" 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">

740

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC740" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">g1_mod_res</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod_res</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs_res</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs_res</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns_res</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="775" 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">

775

</td>

<td class="diff-line-num new_line" data-linenumber="741" 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">

741

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC741" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC742" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="776" 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">

776

</td>

<td class="diff-line-num new_line" data-linenumber="743" 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">

743

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC743" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="777" 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">

777

</td>

<td class="diff-line-num new_line" data-linenumber="744" 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">

744

</td>

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<pre style="margin: 0;"> <span id="LC744" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

778

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC778" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

779

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC779" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'Chr(G1)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">G1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Chr(G2)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">G2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">direction</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">edge weight'</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

780

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC780" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

781

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC781" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'G1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">G2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">direction</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">edge weight'</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

782

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC782" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

783

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC783" class="line" lang="python">    <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

784

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC784" class="line" lang="python">    <span class="n" style="color: #333;">g1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">izip</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

785

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC785" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

786

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<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC786" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

787

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC787" class="line" lang="python">    <span class="n" style="color: #333;">cur_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

788

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC788" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">xrange</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

789

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC789" class="line" lang="python">        <span class="n" style="color: #333;">run_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

790

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC790" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">run</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">run_set</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

791

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC791" class="line" lang="python">            <span class="n" style="color: #333;">g1i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

792

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC792" class="line" lang="python">            <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

793

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC793" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cur_index</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">has_key</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

794

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC794" class="line" lang="python">                <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_index</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

795

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC795" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">DIRECTION_CRICK_STRAND</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

796

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC796" class="line" lang="python">                <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

797

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC797" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

798

</td>

<td class="diff-line-num new_line old" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC798" class="line" lang="python">                <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

745

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC745" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">of</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="799" 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">

799

</td>

<td class="diff-line-num new_line" data-linenumber="746" 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">

746

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC746" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

800

</td>

<td class="diff-line-num new_line old" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC800" class="line" lang="python">            <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">DIRECTION_CRICK_STRAND</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'1'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'-1'</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

747

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC747" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC748" class="line" lang="python">            <span class="n" style="color: #333;">of</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Chr(G1)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">G1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Chr(G2)</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">G2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">direction</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">edge weight</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC749" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

750

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC750" class="line" lang="python">            <span class="n" style="color: #333;">of</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'G1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">G2</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">direction</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">edge weight</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="801" 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">

801

</td>

<td class="diff-line-num new_line" data-linenumber="751" 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">

751

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC751" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

802

</td>

<td class="diff-line-num new_line old" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC802" class="line" lang="python">            <span class="n" style="color: #333;">g1i1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_START'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

803

</td>

<td class="diff-line-num new_line old" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC803" class="line" lang="python">            <span class="n" style="color: #333;">g1i1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">maxint</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_END'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g1i1</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

804

</td>

<td class="diff-line-num new_line old" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC804" class="line" lang="python">            <span class="n" style="color: #333;">g2j1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_START'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

</td>

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805

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<td class="diff-line-num new_line old" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC805" class="line" lang="python">            <span class="n" style="color: #333;">g2j1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">maxint</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_END'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g2j1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

752

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<pre style="margin: 0;">+<span id="LC752" class="line" lang="python">        <span class="n" style="color: #333;">g2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g2</span><span class="p">))))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

753

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<pre style="margin: 0;">+<span id="LC753" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># g1pos = dict(zip(g1, range(len(g1))))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="806" 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">

806

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<td class="diff-line-num new_line" data-linenumber="754" 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">

754

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<pre style="margin: 0;"> <span id="LC754" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

807

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<td class="diff-line-num new_line old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC807" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

808

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<td class="diff-line-num new_line old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC808" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">g1i1</span><span class="p">,</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

809

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<td class="diff-line-num new_line old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC809" class="line" lang="python">                        <span class="n" style="color: #333;">g2j1</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

810

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<td class="diff-line-num new_line old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC810" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

811

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<td class="diff-line-num new_line old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC811" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">g1i1</span><span class="p">,</span> <span class="n" style="color: #333;">g2j1</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

812

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<td class="diff-line-num new_line old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC812" class="line" lang="python">                        <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

755

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<pre style="margin: 0;">+<span id="LC755" class="line" lang="python">        <span class="n" style="color: #333;">cur_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

756

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC756" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">g1_runs</span><span class="p">)):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

757

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<pre style="margin: 0;">+<span id="LC757" class="line" lang="python">            <span class="n" style="color: #333;">run_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

758

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC758" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">run</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">run_set</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

759

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<pre style="margin: 0;">+<span id="LC759" class="line" lang="python">                <span class="n" style="color: #333;">g1i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

760

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC760" class="line" lang="python">                <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

761

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC761" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cur_index</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

762

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC762" class="line" lang="python">                    <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur_index</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

763

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC763" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'+'</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

764

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC764" class="line" lang="python">                    <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

765

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC765" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

766

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC766" class="line" lang="python">                    <span class="n" style="color: #333;">g2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2</span><span class="p">[</span><span class="n" style="color: #333;">g2pos</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endG2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">j</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="813" 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">

813

</td>

<td class="diff-line-num new_line" data-linenumber="767" 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">

767

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC767" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

814

</td>

<td class="diff-line-num new_line old" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC814" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">cur_index</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">run</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

768

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC768" class="line" lang="python">            <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">run</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">direction</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'+'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'1'</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'-1'</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="815" 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">

815

</td>

<td class="diff-line-num new_line" data-linenumber="769" 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">

769

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

816

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC816" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

817

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC817" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

818

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC818" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">usage: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s <DIST FILE> <ALPHA> [ <EDGE WEIGHT THRESHOLD> --repeat-matching (-R) <NUMBER >= 2> --min-cs-size (-M) <NUMBER >= 1> ]'</span> <span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

819

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC819" class="line" lang="python">        <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

820

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC820" class="line" lang="python">   </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

821

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC821" class="line" lang="python">    <span class="n" style="color: #333;">repMatching</span><span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'--repeat-matching'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'-R'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

822

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC822" class="line" lang="python">    <span class="n" style="color: #333;">minCsSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'--min-cs-size'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'-M'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

823

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC823" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

824

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC824" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">minCsSize</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

825

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC825" class="line" lang="python">        <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-M'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'-M'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'--min-cs-size'</span><span class="p">)</span> </span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

826

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC826" class="line" lang="python">        <span class="n" style="color: #333;">minCsSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

827

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC827" class="line" lang="python">        <span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[:</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">:]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

828

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC828" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">repMatching</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

829

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC829" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span> <span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">'Argument --min-cs-size (-M) only valid in '</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

830

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC830" class="line" lang="python">                    <span class="s" style="color: #d14;">'combination with --repeat-matching (-R)'</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

831

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC831" class="line" lang="python">            <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

832

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC832" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

833

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC833" class="line" lang="python">        <span class="n" style="color: #333;">minCsSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

834

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC834" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">repMatching</span><span class="p">:</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

835

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC835" class="line" lang="python">        <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-R'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'-R'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="s" style="color: #d14;">'--repeat-matching'</span><span class="p">)</span> </span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

836

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC836" class="line" lang="python">        <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

837

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC837" class="line" lang="python">        <span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[:</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="p">:]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

838

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC838" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

839

</td>

<td class="diff-line-num new_line old" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC839" class="line" lang="python">        <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

770

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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python">                <span class="n" style="color: #333;">g1i1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_START'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

771

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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python">                <span class="n" style="color: #333;">g1i1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">maxsize</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_END'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g1i1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

772

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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python">                <span class="n" style="color: #333;">g2j1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_START'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

773

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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python">                <span class="n" style="color: #333;">g2j1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">maxsize</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'TELOMERE_END'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">g2j1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="840" 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">

840

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<td class="diff-line-num new_line" data-linenumber="774" 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">

774

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<pre style="margin: 0;"> <span id="LC774" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

841

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<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC841" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># set as global parameter</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

842

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<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC842" class="line" lang="python">    <span class="n" style="color: #333;">alpha</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

843

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<td class="diff-line-num new_line old" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC843" class="line" lang="python">    <span class="n" style="color: #333;">edgeThreshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

775

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC775" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

776

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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python">                    <span class="n" style="color: #333;">of</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

777

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC777" class="line" lang="python">                             <span class="p">(</span><span class="n" style="color: #333;">g1i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">g1i1</span><span class="p">,</span> <span class="n" style="color: #333;">g2j</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">g2j1</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

778

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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="779" style="width: 35px; color: rgba(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="LC779" class="line" lang="python">                    <span class="n" style="color: #333;">of</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">g1i1</span><span class="p">,</span> <span class="n" style="color: #333;">g2j1</span><span class="p">,</span> <span class="n" style="color: #333;">direction</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">weight</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="844" 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">

844

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<td class="diff-line-num new_line" data-linenumber="780" 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">

780

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<pre style="margin: 0;"> <span id="LC780" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

845

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<td class="diff-line-num new_line old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC845" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    logFileName = '%s.log' %(basename(argv[1]).rsplit('.')[0])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

846

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<td class="diff-line-num new_line old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC846" class="line" lang="python">    <span class="n" style="color: #333;">logFileName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.log'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span>                   <span class="c1" style="color: #998; font-style: italic;"># Respect given path</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

847

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<td class="diff-line-num new_line old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC847" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logFileName</span><span class="p">,</span><span class="n" style="color: #333;">filemode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

848

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<td class="diff-line-num new_line old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC848" class="line" lang="python">            <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%(levelname)</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%(asctime)</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">++ </span><span class="si" style="color: #d14;">%(message)</span><span class="s" style="color: #d14;">s"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

781

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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python">                <span class="n" style="color: #333;">cur_index</span><span class="p">[</span><span class="n" style="color: #333;">run</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="849" 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">

849

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<td class="diff-line-num new_line" data-linenumber="782" 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">

782

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC782" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

850

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<td class="diff-line-num new_line old" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC850" class="line" lang="python">    <span class="n" style="color: #333;">greedy</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">10.</span><span class="o" style="font-weight: 600;">**-</span><span class="mi" style="color: #099;">7</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="851" 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">

851

</td>

<td class="diff-line-num new_line" data-linenumber="783" 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">

783

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

852

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<td class="diff-line-num new_line old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC852" class="line" lang="python">    <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDistsAndOrder</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">edgeThreshold</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

853

</td>

<td class="diff-line-num new_line old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC853" class="line" lang="python">    <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

854

</td>

<td class="diff-line-num new_line old" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC854" class="line" lang="python">            <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">greedy</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

784

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC784" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

785

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC785" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">AP</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

786

</td>

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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python">    <span class="n" style="color: #333;">cli</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AP</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC787" class="line" lang="python">    <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-R'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--repeat-matching'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

788

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC788" class="line" lang="python">                     <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'match N repetitions (default: 0)'</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

789

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC789" class="line" lang="python">    <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-M'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--min-cs-size'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'N'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

790

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC790" class="line" lang="python">                     <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'minimal cs size (default: 1)'</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># should be conditional on -R</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

791

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC791" class="line" lang="python">    <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--greedy'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'F'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">10.</span><span class="o" style="font-weight: 600;">**-</span><span class="mi" style="color: #099;">7</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

792

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC792" class="line" lang="python">    <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-e'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--edge_weight_threshold'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

793

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC793" class="line" lang="python">    <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--alpha'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'F'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

794

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC794" class="line" lang="python">    <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'dist_file'</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

795

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC795" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cli</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

796

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC796" class="line" lang="python">    <span class="n" style="color: #333;">AlPHA</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">alpha</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

797

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC797" class="line" lang="python">    <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">repeat_matching</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

798

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC798" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

799

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC799" class="line" lang="python">        <span class="n" style="color: #333;">repMatching</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

800

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC800" class="line" lang="python"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

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<pre style="margin: 0;">+<span id="LC801" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dist_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.log'</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

802

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC802" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%(levelname)</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%(asctime)</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">++ </span><span class="si" style="color: #d14;">%(message)</span><span class="s" style="color: #d14;">s"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

803

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC803" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

804

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC804" class="line" lang="python">    <span class="n" style="color: #333;">multiChrom</span><span class="p">,</span> <span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readDistsAndOrder</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dist_file</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">edge_weight_threshold</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

805

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC805" class="line" lang="python">    <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findRandomRunSequence</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">greedy</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="855" 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">

855

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<td class="diff-line-num new_line" data-linenumber="806" 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">

806

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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python">    <span class="n" style="color: #333;">checkMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="856" 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">

856

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<td class="diff-line-num new_line" data-linenumber="807" 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">

807

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC807" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="857" 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">

857

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<td class="diff-line-num new_line" data-linenumber="808" 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">

808

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC808" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># calculate number of breakpoints only from result of the first matching</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

858

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<td class="diff-line-num new_line old" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC858" class="line" lang="python">    <span class="n" style="color: #333;">bkp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

809

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC809" class="line" lang="python">    <span class="n" style="color: #333;">bkp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span><span class="idiff left right"> </span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="859" 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">

859

</td>

<td class="diff-line-num new_line" data-linenumber="810" 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">

810

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="860" 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">

860

</td>

<td class="diff-line-num new_line" data-linenumber="811" 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">

811

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC811" class="line" lang="python">    <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns_new</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">repeatMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1</span><span class="p">,</span> <span class="n" style="color: #333;">g2</span><span class="p">,</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

861

</td>

<td class="diff-line-num new_line old" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC861" class="line" lang="python">            <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">repMatching</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">minCsSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">greedy</span><span class="p">)</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

812

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC812" class="line" lang="python">            <span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">g2_runs</span><span class="p">,</span> <span class="n" style="color: #333;">dists</span><span class="p">,</span> <span class="n" style="color: #333;">repMatching</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">min_cs_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">greedy</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="862" 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">

862

</td>

<td class="diff-line-num new_line" data-linenumber="813" 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">

813

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="863" 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">

863

</td>

<td class="diff-line-num new_line" data-linenumber="814" 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">

814

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC814" class="line" lang="python">    <span class="n" style="color: #333;">selectedRuns</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">selectedRuns_new</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="864" 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">

864

</td>

<td class="diff-line-num new_line" data-linenumber="815" 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">

815

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

865

</td>

<td class="diff-line-num new_line old" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC865" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

866

</td>

<td class="diff-line-num new_line old" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC866" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># calculate additional values</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

867

</td>

<td class="diff-line-num new_line old" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC867" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

868

</td>

<td class="diff-line-num new_line old" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC868" class="line" lang="python">    </span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="869" 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">

869

</td>

<td class="diff-line-num new_line" data-linenumber="816" 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">

816

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC816" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># sum of weights of adjacencies</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="870" 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">

870

</td>

<td class="diff-line-num new_line" data-linenumber="817" 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">

817

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC817" class="line" lang="python">    <span class="n" style="color: #333;">wAdj</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getWeight</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">])</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="871" 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">

871

</td>

<td class="diff-line-num new_line" data-linenumber="818" 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">

818

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC818" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># sum of weights of all edges of the matching</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

872

</td>

<td class="diff-line-num new_line old" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC872" class="line" lang="python">    <span class="n" style="color: #333;">wEdg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">weight</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">])</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

819

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC819" class="line" lang="python">    <span class="n" style="color: #333;">wEdg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">(<span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">weight</span></span><span class="p"><span class="idiff right">]</span>)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">])</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="873" 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">

873

</td>

<td class="diff-line-num new_line" data-linenumber="820" 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">

820

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC820" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="874" 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">

874

</td>

<td class="diff-line-num new_line" data-linenumber="821" 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">

821

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC821" class="line" lang="python">    <span class="n" style="color: #333;">edg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">,</span> <span class="n" style="color: #333;">selectedRuns</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="875" 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">

875

</td>

<td class="diff-line-num new_line" data-linenumber="822" 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">

822

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

876

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC876" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

877

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC877" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># print matching</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

878

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC878" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

879

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

880

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC880" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    out_file = basename(argv[1])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

881

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC881" class="line" lang="python">    <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># respect given path</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

882

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC882" class="line" lang="python">    <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.matching'</span> <span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">out_file</span><span class="p">[:</span><span class="n" style="color: #333;">out_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)],</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

883

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC883" class="line" lang="python">    <span class="n" style="color: #333;">printMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">hasMultipleChromosomes</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

884

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC884" class="line" lang="python">    <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

885

</td>

<td class="diff-line-num new_line old" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC885" class="line" lang="python">    <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

823

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC823" class="line" lang="python">    <span class="n" style="color: #333;">matchfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dist_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rsplit</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.matching'</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

824

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC824" class="line" lang="python">    <span class="n" style="color: #333;">printMatching</span><span class="p">(</span><span class="n" style="color: #333;">g1_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g2_mod</span><span class="p">,</span> <span class="n" style="color: #333;">g1_runs</span><span class="p">,</span> <span class="n" style="color: #333;">multiChrom</span><span class="p">,</span> <span class="n" style="color: #333;">matchfile</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="886" 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">

886

</td>

<td class="diff-line-num new_line" data-linenumber="825" 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">

825

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC825" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="887" 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">

887

</td>

<td class="diff-line-num new_line" data-linenumber="826" 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">

826

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC826" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="888" 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">

888

</td>

<td class="diff-line-num new_line" data-linenumber="827" 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">

827

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC827" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># print matching scores</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="889" 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">

889

</td>

<td class="diff-line-num new_line" data-linenumber="828" 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">

828

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC828" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="890" 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">

890

</td>

<td class="diff-line-num new_line" data-linenumber="829" 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">

829

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC829" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

891

</td>

<td class="diff-line-num new_line old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC891" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">((</span><span class="s" style="color: #d14;">'FFAdj-MCS finished. Breakpoint distance between G1 and G2'</span> <span class="o" style="font-weight: 600;">+</span> \</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

892

</td>

<td class="diff-line-num new_line old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC892" class="line" lang="python">            <span class="s" style="color: #d14;">' is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s with #edg = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, adj(M) = </span><span class="si" style="color: #d14;">%.3</span><span class="s" style="color: #d14;">f and edg(M) = </span><span class="si" style="color: #d14;">%.3</span><span class="s" style="color: #d14;">f'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">bkp</span><span class="p">,</span> <span class="n" style="color: #333;">edg</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

893

</td>

<td class="diff-line-num new_line old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC893" class="line" lang="python">                <span class="n" style="color: #333;">wAdj</span><span class="p">,</span> <span class="n" style="color: #333;">wEdg</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

894

</td>

<td class="diff-line-num new_line old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC894" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

895

</td>

<td class="diff-line-num new_line old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC895" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'#bkp</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">#edg</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">adj</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">edg'</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

896

</td>

<td class="diff-line-num new_line old" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC896" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.6</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.6</span><span class="s" style="color: #d14;">f'</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">bkp</span><span class="p">,</span> <span class="n" style="color: #333;">edg</span><span class="p">,</span> <span class="n" style="color: #333;">wAdj</span><span class="p">,</span> <span class="n" style="color: #333;">wEdg</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

830

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC830" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">((</span><span class="s" style="color: #d14;">'FFAdj-MCS finished. Breakpoint distance between G1 and G2'</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

831

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC831" class="line" lang="python">              <span class="s" style="color: #d14;">' is </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s with #edg = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, adj(M) = </span><span class="si" style="color: #d14;">%.3</span><span class="s" style="color: #d14;">f and edg(M) = </span><span class="si" style="color: #d14;">%.3</span><span class="s" style="color: #d14;">f'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

832

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC832" class="line" lang="python">             <span class="p">(</span><span class="n" style="color: #333;">bkp</span><span class="p">,</span> <span class="n" style="color: #333;">edg</span><span class="p">,</span> <span class="n" style="color: #333;">wAdj</span><span class="p">,</span> <span class="n" style="color: #333;">wEdg</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="897" 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">

897

</td>

<td class="diff-line-num new_line" data-linenumber="833" 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">

833

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC833" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

834

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC834" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'#bkp</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">#edg</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">adj</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">edg'</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

835

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC835" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.6</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.6</span><span class="s" style="color: #d14;">f'</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">bkp</span><span class="p">,</span> <span class="n" style="color: #333;">edg</span><span class="p">,</span> <span class="n" style="color: #333;">wAdj</span><span class="p">,</span> <span class="n" style="color: #333;">wEdg</span><span class="p">))</span></span></pre>

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