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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/e3d760eb2d63b78ef61fde488783c2e5aa7a856b">e3d760eb</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-16T10:41:53Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 6.0.7+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/103ce9991502188909a12c477ec08f1e94280bc3">103ce999</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-16T10:41:53Z</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/afb46e8e048a297bbc8d31f4e0663e98a5302af8">afb46e8e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-16T10:41:54Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/6.0.7+dfsg'

Update to upstream version '6.0.7+dfsg'

with Debian dir 1e9b2d7e350052776d074aaac6c7e7399ff39ef4</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/12c0b78f5c67ca109a891b9a2961bc79ae571963">12c0b78f</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-16T10:41:54Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/073c997d4bd46dddc5a09c76ee4cb77bd81c1821">073c997d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-16T11:06:46Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use 2to3 to port to Python3

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/46b56795faef96c95bb86901b1e453561560c447">46b56795</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-09-16T11:37:31Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">s/maxint/maxsize/g

</pre>

</li>

</ul>

<h4>20 changed files:</h4>

<ul>

<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="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<span class="deleted-file">

−

debian/compat

</span>

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">

<span class="new-file">

+

debian/patches/2to3.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<span class="new-file">

+

debian/patches/series

</span>

</a>

</li>

<li class="file-stats">

<a href="#36a872632d316444cc5323d30503cc0b7ef33071">

manual.html

</a>

</li>

<li class="file-stats">

<a href="#c9e37a96ac72f9ef076d7a41a57470524d63b36e">

proteinortho6.pl

</a>

</li>

<li class="file-stats">

<a href="#365702ff19fca4ff0a844ce49b9407eece5bcccb">

src/proteinortho2html.pl

</a>

</li>

<li class="file-stats">

<a href="#d9308efe3c187e986d67db455c6ee886ad8d11fe">

src/proteinortho2tree.pl

</a>

</li>

<li class="file-stats">

<a href="#d0cbc2488744231506d0c284dad99f8cc4078553">

src/proteinortho2xml.pl

</a>

</li>

<li class="file-stats">

<a href="#01410a3f6d57c666b088e9dabd2cfaa1863fc64b">

src/proteinortho_do_mcl.pl

</a>

</li>

<li class="file-stats">

<a href="#232293c8a051e6a419f2acfdc302a6db199fbaef">

src/proteinortho_extract_from_graph.pl

</a>

</li>

<li class="file-stats">

<a href="#e52fa9f6246a270e3b0a6a888a797d22f02e2532">

src/proteinortho_ffadj_mcs.py

</a>

</li>

<li class="file-stats">

<a href="#4f473eed99a366a7f281ddc66ff63e30800ea98b">

src/proteinortho_formatUsearch.pl

</a>

</li>

<li class="file-stats">

<a href="#3439148ea7017354388f7c55043cc84986c1c394">

src/proteinortho_grab_proteins.pl

</a>

</li>

<li class="file-stats">

<a href="#ea348db3b0f7b6f9afd028c87edc31b9e84dcb72">

src/proteinortho_singletons.pl

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#1c497fbb3a46b78edf04cc2a2fa33f67e3ffbe2a"><strong>CHANGELOG</strong></a>

<hr>

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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">@@ -217,3 +217,7 @@</td>

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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">

217

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<td class="diff-line-num 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">

217

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">        proteinortho_grab_proteins.pl speedup for -exact and a given proteinortho file</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="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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext">        proteinortho6.pl replaced chomp with s/[\r\n]+$//</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="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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

<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext">        proteinortho_clustering.cpp fix bug that only uses lapack if -pld is set, regardless of the value.</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="220" style="width: 35px; color: rgba(0,0,0,0.3); 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="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

220

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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="LC220" class="line" lang="plaintext">    11. Sept (uid: 3813)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_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">

221

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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="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>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); 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="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

222

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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="LC222" class="line" lang="plaintext">    -p=blastp is now alias of blastp+ and legacy blast is now -p=blastp_legacy (blastn is equivalent)</span>

</pre>

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</tr>

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

<td class="diff-line-num new old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

223

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

</td>

</tr>

</table>

<br>

</li>

<li id="ff6936350384213d6f693f4d604134188ce088c8">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#ff6936350384213d6f693f4d604134188ce088c8"><strong>CHANGEUID</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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

</td>

<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="plaintext">3<span class="idiff left right">697</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="plaintext">3<span class="idiff left right">813</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>

<hr>

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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="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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,7 +132,7 @@ 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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC132" 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">

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133

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<pre style="margin: 0;"> <span id="LC133" 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="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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<pre style="margin: 0;"> <span id="LC134" 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">

135

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<td class="diff-line-num new_line old" 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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<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;">-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;">||</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 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="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="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 right">-</span>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;">||</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 old_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">

136

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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">

136

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<pre style="margin: 0;"> <span id="LC136" 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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<pre style="margin: 0;"> <span id="LC137" 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>

</pre>

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<td class="diff-line-num old_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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<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="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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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,8 +39,8 @@ You can also send a mail to lechner@staff.uni-marburg.de.</td>

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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="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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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></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="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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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="gh" style="color: #999;"># Installation</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="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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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Proteinortho comes with precompiled binaries of all executables (Linux/x86) so <span class="idiff left right">just run the</span> proteinortho6.pl in the downloaded directory.**</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown">You could also move all executables to your favorite <span class="idiff left right">bin </span>directory (e.g. with make install PREFIX=/home/paul/bin).</span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**Proteinortho comes with precompiled binaries of all executables (Linux/x86) so <span class="idiff left right">you should be able to run perl</span> proteinortho6.pl in the downloaded directory.**</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">You could also move all executables to your favorite directory (e.g. with make install PREFIX=/home/paul/bin).</span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown">If you cannot execute the src/BUILD/Linux_x86_64/proteinortho_clustering, then you have to recompile with make, see the section 2. Building and installing proteinortho from source.</span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC46" 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">@@ -73,6 +73,21 @@ If you need brew (see [here](https://brew.sh/index_de))</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### Easy installation with dpkg (root privileges are required)</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown">The deb package can be downloaded here: <span class="p">[</span><span class="nv" style="color: #008080;">https://packages.debian.org/unstable/proteinortho</span><span class="p">](</span><span class="sx" style="color: #d14;">https://packages.debian.org/unstable/proteinortho</span><span class="p">)</span>.</span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown">Afterwards the deb package can be installed with <span class="sb" style="color: #d14;">`sudo dpkg -i proteinortho*deb`</span>.</span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### *(Easy installation with apt-get)*</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"></span>

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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">

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**! Disclamer: Work in progress !**</span></span>

</pre>

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<td class="diff-line-num new old_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">

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<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">

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with `sudo apt-get install proteinortho` (currently this installes the outdated version v5.16b)*</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### 1. Prerequisites</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown">Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.</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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,7 +109,7 @@ 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="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="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">

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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="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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<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">

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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_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="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">

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="p">   -</span> Python v2.6.0 or higher to include synteny analysis (to test this, type 'python -V' in the command line) </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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<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="LC97" class="line" lang="markdown"><span class="p">   -</span> Perl <span class="idiff left">modules: Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with </span><span class="sb" style="color: #d14;"><span class="idiff right">`cpan install Thread::Queue</span>`</span> )</span>

</pre>

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<td class="diff-line-num new old_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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<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">

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

</pre>

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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">

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

</pre>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"><span class="nt" style="color: #000080;"><br></span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,9 +128,9 @@ Proteinortho uses standard software which is often installed already or is part</td>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"></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">

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

</pre>

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

</pre>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown">  Here you <span class="nt" style="color: #000080;"><span class="idiff left"><i></span></span><span class="idiff">can</span><span class="nt" style="color: #000080;"><span class="idiff right"></i></span></span> 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>

</pre>

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<td class="diff-line-num new old_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">

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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="markdown">  Here you <span class="idiff left right">can</span> 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>

</pre>

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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">

117

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown">  </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">

118

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown">  If you dont have <span class="idiff left right">one (or you have no root permissions), then 'make' will automatically compile a lapack (v3.8.0)</span> for you !</span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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>

</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="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">

136

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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>

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -281,7 +296,7 @@ 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="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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<td class="diff-line-num new_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="LC296" 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="282" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="LC297" 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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<td class="diff-line-num old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); 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="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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;">      </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); 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="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - blastn<span class="idiff left right">,blastp,tblastx</span> : 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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<td class="diff-line-num new old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC299" class="line" lang="markdown"><span class="sb" style="color: #d14;">        - blastn<span class="idiff left right">_legacy,blastp_legacy,tblastx_legacy</span> : 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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<td class="diff-line-num old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); 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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

286

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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;">        - blastn+,blastp+,tblastx+ : standard blast family (shell commands: blastn,blastp,tblastx)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<pre style="margin: 0;"> <span id="LC302" 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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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

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

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">proteinortho (6.0.7+dfsg-1) UNRELEASED; urgency=medium</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * debhelper-compat 12</span>

</pre>

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

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Use 2to3 to port to Python3</span>

</pre>

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

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Mon, 16 Sep 2019 12:41:53 +0200</span>

</pre>

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8

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

</pre>

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1

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9

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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>

</pre>

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2

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num 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">

3

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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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  [ Paul Klemm ]</span>

</pre>

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<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>

deleted

</a>

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1

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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="LC1" class="line" lang="plaintext">12</span></pre>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>

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<td class="diff-line-num 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">

3

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></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="plaintext">Section: science</span>

</pre>

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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="plaintext">Priority: optional</span>

</pre>

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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="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 12~</span>),</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>

</pre>

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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="plaintext">               ncbi-blast+,</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="plaintext">               liblapack-dev | libatlas-base-dev | liblapack.so,</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="plaintext">               diamond-aligner</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="555c85016bd79aa8bbb523506af81b69d9c69534">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>

<hr>

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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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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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="LC2" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="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="diff"><span class="p">Last-Update: Mon, 16 Sep 2019 12:41:53 +0200</span></span>

</pre>

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

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

4

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>

</pre>

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

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/src/proteinortho_ffadj_mcs.py</span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/proteinortho_ffadj_mcs.py</span></span>

</pre>

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

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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">

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,9 +1,9 @@</span></span>

</pre>

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

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

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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

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

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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="LC10" class="line" lang="diff"> </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from sys import stdout, stderr, exit, argv, maxint</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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

<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>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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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="LC13" class="line" lang="diff"> from copy import deepcopy</span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from itertools import izip, product</span></span>

</pre>

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

</td>

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

16

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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="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from itertools import product</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="diff"> from os.path import basename, dirname</span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="diff"> from random import randint</span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> from math import ceil</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

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

</pre>

</td>

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

</td>

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

</td>

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff">         if len(self.weight) > 1:</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff">             adjTerm = sum([self.weight[i] * self.weight[i+1] for i in</span>

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<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>

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<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>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff">         edgeTerm = sum([w **2  for w in self.weight])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> #        edgeTerm = max(self.weight)**2</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff">         return alpha * adjTerm + (1-alpha) * edgeTerm</span>

</pre>

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<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>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff">         if edgeWeight < edgeThreshold:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff">             continue</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>

</pre>

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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>

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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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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff">             g1_chromosomes[chr1] = set()</span>

</pre>

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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 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="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 new new_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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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff">             g2_chromosomes[chr2] = set()</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff">         g1_chromosomes[chr1].add(g1)</span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff">     # add telomeres</span>

</pre>

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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="diff">     for t1, t2 in product(tel1, tel2):</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="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 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">

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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 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="diff">             res[t1] = dict()</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC48" class="line" lang="diff">         res[t1][t2] = (DIRECTION_BOTH_STRANDS, 1)</span>

</pre>

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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="diff"> </span>

</pre>

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<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">

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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 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">

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

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

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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> #        (0,      (DIRECTION_WATSON_STRAND, 1)), </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> #        (0,      (DIRECTION_CRICK_STRAND, 1))])</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC62" class="line" lang="diff"> #        (0,      (DIRECTION_WATSON_STRAND, 1)),</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#        (maxint, (DIRECTION_CRICK_STRAND, 1)), </span></span>

</pre>

</td>

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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>

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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>

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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>

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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>

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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>

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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>

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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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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff">     return telomeres, g</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff">         </span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> def insertIntoRunList(runs, runList):</span>

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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>

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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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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff">     for run in runs:</span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff">         keys.insert(i, run.getWeight(alpha))</span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>

</pre>

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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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<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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<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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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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<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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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff">     r_counter = 0 </span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff">     prev_run = None</span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff">     c_adj = 0</span>

</pre>

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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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<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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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff">         if not g1_runs[i]:</span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff">             continue</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="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="diff"><span class="p">@@ -213,7 +213,7 @@</span> def checkMatching(g1, g2, g1_runs, g2_ru</span>

</pre>

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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="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>

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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>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff">         </span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff">     logging.info('Number of adjacencies is %s in matching of size %s.' %(c_adj,</span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff">         len(g1)))</span>

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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>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for j in xrange(len(g2)):</span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for j in range(len(g2)):</span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff">         if not g2_runs[j]:</span>

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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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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff">         if len(g2_runs[j]) > 1:</span>

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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>

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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>

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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>

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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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<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>

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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>

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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>

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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>

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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>

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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>

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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>

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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>

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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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<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>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff">         g1i = g1[i]</span>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff">         g1i2 = g1[i+1]</span>

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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>

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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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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff">             g2i2 = run_ends[g1i2][1]</span>

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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>

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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>

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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>

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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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<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>

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

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> def getAllRuns(g1, g2, d):</span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff">     g1_runs = [set() for _ in g1]</span>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff">     g2_runs = [set() for _ in g2]</span>

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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>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff">     reportedRuns= list()</span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff">         curPos = g1[i] </span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff">         </span>

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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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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> </span>

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC169" class="line" lang="diff">         # if no edge exists, nothing has to be done...</span>

</pre>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff">         if e:</span>

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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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<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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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff">                 if (direction, g2_gene) not in forbiddenRunStarts:</span>

</pre>

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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 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">

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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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<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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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff">  </span>

</pre>

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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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<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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<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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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff">         i = g1pos[m.startG1] + k</span>

</pre>

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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>

</pre>

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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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<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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<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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<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>

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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff">     newRuns = set()</span>

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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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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff">     mod_g1 = list(mod_g1)</span>

</pre>

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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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<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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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff">         g1i = mod_g1[x]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff">         i = g1pos[g1i]</span>

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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff">         if len(g1) < i+2:</span>

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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>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"> def findRandomRunSequence(g1, g2, dists, topXperCent):</span>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff">     g2dists = dict()</span>

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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>

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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>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff">             if g2j not in g2dists:</span>

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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>

</pre>

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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>

</pre>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff">                     mod_g1.remove(g)</span>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="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>

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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>

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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>

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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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<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>

</pre>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff">                     runList, res)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff">   </span>

</pre>

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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff">     if res: </span>

</pre>

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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>

</pre>

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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>

</pre>

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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>

</pre>

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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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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff">         logging.info('Matching finished, but no runs found. Empty input?')</span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> </span>

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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>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff">     selectedRuns_res = list()</span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> </span>

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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>

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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>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> </span>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff">             g1i = g1_mod[i]</span>

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

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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>

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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>

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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>

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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>

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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>

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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>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff">             x = set()</span>

</pre>

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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>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff">                 x.update(g1_runs_res[g1pos_res[g1i]])</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff">                 x.update(g1_runs[g1pos[g1i]])</span>

</pre>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff">             g1_runs_new.append(x)</span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff">         for g2j in g2_mod_new:</span>

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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>

</pre>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff">                 x.update(g2_runs_res[g2pos_res[g2j]])</span>

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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>

</pre>

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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>

</pre>

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

</pre>

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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>

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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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<td class="diff-line-num new new_line" data-linenumber="352" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC352" class="line" lang="diff">     if hasMultipleChromosomes:</span>

</pre>

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353

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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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354

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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>

</pre>

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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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<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="diff">     cur_index = dict()</span>

</pre>

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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 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="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 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="diff">         run_set = g1_runs[i]</span>

</pre>

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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 new new_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC370" class="line" lang="diff">             g1i = g1[i]</span>

</pre>

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371

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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff">             j = 0</span>

</pre>

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372

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if cur_index.has_key(run):</span></span>

</pre>

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373

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if run in cur_index:</span></span>

</pre>

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374

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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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375

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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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376

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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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377

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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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378

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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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379

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> </span>

</pre>

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380

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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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381

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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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382

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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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383

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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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<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>

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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            g2j1 = g2j[1] == maxsize and 'TELOMERE_END' or g2j1</span></span>

</pre>

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386

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> </span>

</pre>

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387

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff">             if hasMultipleChromosomes:</span>

</pre>

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388

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                print >> f, '%s\t%s\t%s\t%s\t%s\t%s' %(g1i[0], g1i1, g2j[0],</span></span>

</pre>

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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">

389

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<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>

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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

390

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<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>

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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">

391

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<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>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

392

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

</pre>

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

</td>

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

393

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<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>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

394

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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="LC394" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                        run.weight[j])</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

395

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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="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>

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

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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

396

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                        run.weight[j]), file=f)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

397

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

<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

398

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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="LC398" class="line" lang="diff">             cur_index[run] = j+1</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

399

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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="LC399" class="line" lang="diff"> </span>

</pre>

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

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

400

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> if __name__ == '__main__':</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

401

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff">     if len(argv) < 3 or len(argv) > 8:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

402

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<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>

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

</td>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

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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="LC405" class="line" lang="diff">    </span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff">     repMatching= '--repeat-matching' in argv or '-R' in argv</span>

</pre>

</td>

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

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<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

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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="LC407" class="line" lang="diff"><span class="p">@@ -826,8 +826,8 @@</span> if __name__ == '__main__':</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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="diff">         minCsSize = int(argv[pos+1])</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

409

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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="LC409" class="line" lang="diff">         argv = argv[:pos] + argv[pos+2:]</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff">         if not repMatching:</span>

</pre>

</td>

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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>

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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>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff">             exit(1)</span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff">     else:</span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff">         minCsSize = 1</span>

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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>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff">     # sum of weights of adjacencies</span>

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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>

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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>

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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>

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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>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff">     edg = sum(map(len, selectedRuns))</span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="p">@@ -892,6 +892,6 @@</span> if __name__ == '__main__':</span>

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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>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff">                 wAdj, wEdg))</span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"> </span>

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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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<td class="diff-line-num new new_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">

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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<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 new new_line" data-linenumber="434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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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/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2to3.patch</span></pre>

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<br>

</li>

<li id="36a872632d316444cc5323d30503cc0b7ef33071">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#36a872632d316444cc5323d30503cc0b7ef33071"><strong>manual.html</strong></a>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,8 +58,8 @@ You can also send a mail to lechner@staff.uni-marburg.de.</p></td>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="html"><span class="nt" style="color: #000080;"><h1</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"installation"</span><span class="nt" style="color: #000080;">></span>Installation<span class="nt" style="color: #000080;"></h1></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Proteinortho comes with precompiled binaries of all executables (Linux/x86) so <span class="idiff left right">just run the</span> proteinortho6.pl in the downloaded directory.<span class="nt" style="color: #000080;"></strong></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="html">You could also move all executables to your favorite <span class="idiff left right">bin </span>directory (e.g. with make install PREFIX=/home/paul/bin).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>Proteinortho comes with precompiled binaries of all executables (Linux/x86) so <span class="idiff left right">you should be able to run perl</span> proteinortho6.pl in the downloaded directory.<span class="nt" style="color: #000080;"></strong></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="html">You could also move all executables to your favorite directory (e.g. with make install PREFIX=/home/paul/bin).</span>

</pre>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="html">If you cannot execute the src/BUILD/Linux<span class="nt" style="color: #000080;"><em></span>x86<span class="nt" style="color: #000080;"></em></span>64/proteinortho_clustering, then you have to recompile with make, see the section 2. Building and installing proteinortho from source.<span class="nt" style="color: #000080;"></p></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,6 +95,20 @@ If you cannot execute the src/BUILD/Linux<em>x86</em>64/proteinortho_clustering,</td>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="html"></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="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easyinstallationwithdpkgrootprivilegesarerequired"</span><span class="nt" style="color: #000080;">></span>Easy installation with dpkg (root privileges are required)<span class="nt" style="color: #000080;"></h4></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>The deb package can be downloaded here: <span class="nt" style="color: #000080;"><a</span> <span class="na" style="color: #008080;">href=</span><span class="s" style="color: #d14;">"https://packages.debian.org/unstable/proteinortho"</span><span class="nt" style="color: #000080;">></span>https://packages.debian.org/unstable/proteinortho<span class="nt" style="color: #000080;"></a></span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="html">Afterwards the deb package can be installed with <span class="nt" style="color: #000080;"><code></span>sudo dpkg -i proteinortho*deb<span class="nt" style="color: #000080;"></code></span>.<span class="nt" style="color: #000080;"></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"easyinstallationwithaptget"</span><span class="nt" style="color: #000080;">><em></span>(Easy installation with apt-get)<span class="nt" style="color: #000080;"></em></h4></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="html"><span class="nt" style="color: #000080;"><p><strong></span>! Disclamer: Work in progress !<span class="nt" style="color: #000080;"></strong></span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="html"><span class="nt" style="color: #000080;"><em></span>proteinortho will be released to stable with Debian 11 (~2021), then proteinortho can be installed with <span class="nt" style="color: #000080;"><code></span>sudo apt-get install proteinortho<span class="nt" style="color: #000080;"></code></span> (currently this installes the outdated version v5.16b)<span class="nt" style="color: #000080;"></em></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="html"><span class="nt" style="color: #000080;"><p><br></p></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"1prerequisites"</span><span class="nt" style="color: #000080;">></span>1. Prerequisites<span class="nt" style="color: #000080;"></h4></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Proteinortho uses standard software which is often installed already or is part of then package repositories and can thus easily be installed. The sources come with a precompiled version of Proteinortho for 64bit Linux.<span class="nt" style="color: #000080;"></p></span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,7 +142,7 @@ If you cannot execute the src/BUILD/Linux<em>x86</em>64/proteinortho_clustering,</td>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="html"><span class="nt" style="color: #000080;"><li><p></span>Python v2.6.0 or higher to include synteny analysis (to test this, type 'python -V' in the command line) <span class="nt" style="color: #000080;"></p></li></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="html"></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">

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<td class="diff-line-num new_line old" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-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="html"><span class="nt" style="color: #000080;"><li><p></span>Perl <span class="idiff left">modules: Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with </span><span class="nt" style="color: #000080;"><span class="idiff"><code></span></span><span class="idiff right">cpan install Thread::Queue</span><span class="nt" style="color: #000080;"></code></span> )</span>

</pre>

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<td class="diff-line-num new old_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">

</td>

<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="html"><span class="nt" style="color: #000080;"><li><p></span>Perl <span class="idiff left">standard modules (these should come with Perl): Thread::Queue, File::Basename, Pod::Usage, threads (if you miss one just install with </span><span class="nt" style="color: #000080;"><span class="idiff"><code></span></span><span class="idiff right">cpan install ...</span><span class="nt" style="color: #000080;"></code></span> )</span>

</pre>

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132

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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="html"><span class="nt" style="color: #000080;"></details></p></li></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="html"><span class="nt" style="color: #000080;"></ul></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">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,9 +168,9 @@ If you cannot execute the src/BUILD/Linux<em>x86</em>64/proteinortho_clustering,</td>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="html"></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="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">

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="html"><span class="nt" style="color: #000080;"><h4</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"2buildingandinstallingproteinorthofromsourcelinuxandosx"</span><span class="nt" style="color: #000080;">></span>2. Building and installing proteinortho from source (linux and osx)<span class="nt" style="color: #000080;"></h4></span></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="html"></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">

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<td class="diff-line-num new_line old" 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="LC157" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Here you <span class="nt" style="color: #000080;"><span class="idiff left"><i></span></span><span class="idiff">can</span><span class="nt" style="color: #000080;"><span class="idiff right"></i></span></span> 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 class="nt" style="color: #000080;"></p></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); 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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Here you <span class="idiff left right">can</span> 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 class="nt" style="color: #000080;"></p></span></span>

</pre>

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<td class="diff-line-num old_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">

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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">

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="html"></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">

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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="LC159" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If you dont have <span class="idiff left right">one (or you have no root permissions), then 'make' will automatically compile a lapack (v3.8.0)</span> for you !<span class="nt" style="color: #000080;"></p></span></span>

</pre>

</td>

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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="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">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If you dont have <span class="idiff left right">Lapack, then 'make' will automatically compiles Lapack v3.8.0</span> for you !<span class="nt" style="color: #000080;"></p></span></span>

</pre>

</td>

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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">

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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">

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="html"></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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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>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>

</pre>

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162

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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">

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="html"><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></p></span></span>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -345,7 +359,7 @@ blast. 3 -> run the clustering.</p></li></ul></td>

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<td class="diff-line-num old_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">

345

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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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<pre style="margin: 0;"> <span id="LC359" class="line" lang="html"><span class="nt" style="color: #000080;"><p><details></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">

346

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<td class="diff-line-num new_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="html">  <span class="nt" style="color: #000080;"><summary></span>show all algorithms (Click to expand)<span class="nt" style="color: #000080;"></summary></p></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

347

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num old old_line" 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">

348

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>- blastn<span class="idiff left right">,blastp,tblastx</span> : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC362" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>- blastn<span class="idiff left right">_legacy,blastp_legacy,tblastx_legacy</span> : legacy blast family (shell commands: blastall -) family. The suffix 'n' or 'p' indicates nucleotide or protein input files.</span>

</pre>

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<td class="diff-line-num 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">

349

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363

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num old_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">

350

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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">

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="html">- blastn+,blastp+,tblastx+ : standard blast family (shell commands: blastn,blastp,tblastx)</span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="html">family. The suffix 'n' or 'p' indicates nucleotide or protein input files.</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="c9e37a96ac72f9ef076d7a41a57470524d63b36e">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#c9e37a96ac72f9ef076d7a41a57470524d63b36e"><strong>proteinortho6.pl</strong></a>

The diff for this file was not included because it is too large.

<br>

</li>

<li id="365702ff19fca4ff0a844ce49b9407eece5bcccb">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#365702ff19fca4ff0a844ce49b9407eece5bcccb"><strong>src/proteinortho2html.pl</strong></a>

<hr>

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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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>

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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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</span></span>

</pre>

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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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#pk</span></span>

</pre>

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<td class="diff-line-num 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">

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">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

</pre>

</td>

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<br>

</li>

<li id="d9308efe3c187e986d67db455c6ee886ad8d11fe">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#d9308efe3c187e986d67db455c6ee886ad8d11fe"><strong>src/proteinortho2tree.pl</strong></a>

<hr>

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1

</td>

<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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>

</pre>

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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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</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">

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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="perl"></span>

</pre>

</td>

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<td class="diff-line-num 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">

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

<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">

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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>

</td>

</tr>

</table>

<br>

</li>

<li id="d0cbc2488744231506d0c284dad99f8cc4078553">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#d0cbc2488744231506d0c284dad99f8cc4078553"><strong>src/proteinortho2xml.pl</strong></a>

<hr>

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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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>

</pre>

</td>

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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">

</td>

<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

</td>

<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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</span></span>

</pre>

</td>

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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

</td>

<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

</td>

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

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

</pre>

</td>

</tr>

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<td class="diff-line-num 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">

3

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

</td>

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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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span> <span class="p">"</span><span class="s2" style="color: #d14;">all</span><span class="p">";</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="01410a3f6d57c666b088e9dabd2cfaa1863fc64b">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#01410a3f6d57c666b088e9dabd2cfaa1863fc64b"><strong>src/proteinortho_do_mcl.pl</strong></a>

<hr>

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1

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>

</pre>

</td>

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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">

</td>

<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

</td>

<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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</span></span>

</pre>

</td>

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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

</td>

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

<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#pk</span></span>

</pre>

</td>

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<td class="diff-line-num 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">

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

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"></span>

</pre>

</td>

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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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="232293c8a051e6a419f2acfdc302a6db199fbaef">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#232293c8a051e6a419f2acfdc302a6db199fbaef"><strong>src/proteinortho_extract_from_graph.pl</strong></a>

<hr>

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1

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>

</pre>

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</td>

<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

</td>

<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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</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

</td>

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

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

</pre>

</td>

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<td class="diff-line-num 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">

3

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>

</pre>

</td>

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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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="e52fa9f6246a270e3b0a6a888a797d22f02e2532">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#e52fa9f6246a270e3b0a6a888a797d22f02e2532"><strong>src/proteinortho_ffadj_mcs.py</strong></a>

<hr>

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1

</td>

<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">

</td>

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

<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">python</span></span></span>

</pre>

</td>

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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">

</td>

<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

</td>

<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">env python2.7</span></span></span>

</pre>

</td>

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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

</td>

<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>

</td>

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<td class="diff-line-num 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">

3

</td>

<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

</td>

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

<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;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">exit</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">maxint</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="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

</td>

<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

</td>

<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>

</tr>

</table>

<br>

</li>

<li id="4f473eed99a366a7f281ddc66ff63e30800ea98b">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#4f473eed99a366a7f281ddc66ff63e30800ea98b"><strong>src/proteinortho_formatUsearch.pl</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<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

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</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="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">

</td>

<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

</td>

<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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</span></span>

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC2" 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="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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</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="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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="3439148ea7017354388f7c55043cc84986c1c394">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#3439148ea7017354388f7c55043cc84986c1c394"><strong>src/proteinortho_grab_proteins.pl</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<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

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</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="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">

</td>

<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

</td>

<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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</span></span>

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#pk</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num 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">

3

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC3" 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="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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="ea348db3b0f7b6f9afd028c87edc31b9e84dcb72">

<a href="https://salsa.debian.org/med-team/proteinortho/compare/1e3a8b8e4293c01d8302b126fbea38f0c1399f0b...46b56795faef96c95bb86901b1e453561560c447#ea348db3b0f7b6f9afd028c87edc31b9e84dcb72"><strong>src/proteinortho_singletons.pl</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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

<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

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</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="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">

</td>

<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

</td>

<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="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/<span class="idiff left right">env </span>perl</span></span>

</pre>

</td>

</tr>

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

<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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC2" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</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="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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span> <span class="p">"</span><span class="s2" style="color: #d14;">all</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="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

</td>

<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

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"></span>

</pre>

</td>

</tr>

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