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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/ragout">Debian Med / ragout</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61">c8991daa</a></strong>
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<span>by Steffen Möller</span>
<i>at 2020-01-04T19:08:56+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Another attempt at 2.2
</pre>
</li>
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">
debian/patches/2to3.patch
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<li class="file-stats">
<a href="#49cce42d8923c0f68a3e48ad8f9039dfa5479cee">
<span class="new-file">
+
debian/patches/adjustSetupParsingBinaries.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#5eaab3a6d332a70f8f7ab5b488590b063dc6f4c8">
debian/ragout.install
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ragout (2.2-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ragout (2.2-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [Andreas Tille]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * debhelper-compat 12</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.4.0</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> * Use 2to3 to port to Python3</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> Closes: #938330</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> TODO: Does not work yet - see</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> https://github.com/fenderglass/Ragout/issues/52</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Use 2to3 to port to Python3 (Closes: #938330)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> also see https://github.com/fenderglass/Ragout/issues/52</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [Steffen Moeller]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Not having Python install binaries in setup.py, chaning</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> d/ragout.install accordingly</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * bin/ragout was still about to invoke python2</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * not allowing bin/ragout to change $PATH </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * demoted sibelia to recommends runtime dependency as there are</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> modules that don't use it.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> TODO: Find out what happened to</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> https://salsa.debian.org/med-team/sibelia</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> which is not in new or main.</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- <span class="idiff left right">Andreas Tille <tille@debian.org> Thu, 05 Sep 2019 10:06:47 +02</span>00</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> -- <span class="idiff left right">Steffen Moeller <moeller@debian.org> Sat, 04 Jan 2020 19:07:58 +01</span>00</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">ragout (2.1.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,8 +17,9 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> sibelia,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> python3-networkx (>= 2.2)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Recommends:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> sibelia</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Description: Reference-Assisted Genome Ordering UTility</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> Ragout (Reference-Assisted Genome Ordering UTility) is a tool for</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> chromosome-level scaffolding using multiple references. Given initial</span>
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<a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,8 +43,10 @@ SyntaxError: invalid or missing encoding declaration for 'bin/ragout-maf2synteny</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff">Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff">--- a/ragout/assembly_graph/assembly_refine.py</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/assembly_graph/assembly_refine.py</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff">Index: ragout/ragout/assembly_graph/assembly_refine.py</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/assembly_graph/assembly_refine.py</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/assembly_graph/assembly_refine.py</span></span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span> import re</span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> import logging</span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> from collections import namedtuple</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,8 +74,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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72
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> queue.put(src)</span>
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73
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> visited = set([src])</span>
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74
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"> parent = {src : src}</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/breakpoint_graph/breakpoint_graph.py</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/breakpoint_graph/breakpoint_graph.py</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/breakpoint_graph/breakpoint_graph.py</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></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;">--- ragout.orig/ragout/breakpoint_graph/breakpoint_graph.py</span></span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/breakpoint_graph/breakpoint_graph.py</span></span>
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77
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"><span class="p">@@ -87,12 +87,10 @@</span> class BreakpointGraph(object):</span>
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78
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> def genomes_chrs_support(self, node_1, node_2):</span>
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79
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> if not self.bp_graph.has_edge(node_1, node_2):</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -155,8 +159,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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155
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> fout.write(" [" + ", ".join(extra) + "]")</span>
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156
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"> fout.write(";\n")</span>
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157
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="diff"> fout.write("}")</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/breakpoint_graph/chimera_detector.py</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/breakpoint_graph/chimera_detector.py</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/breakpoint_graph/chimera_detector.py</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/breakpoint_graph/chimera_detector.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/breakpoint_graph/chimera_detector.py</span></span>
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160
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span> This module tries to detect missassemble</span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="diff"> in input sequences and breaks them if neccesary</span>
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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 unfold js-unfold new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -209,8 +215,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="diff"> for genome in common_genomes:</span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="diff"> if chr_1[genome] != chr_2[genome]:</span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="diff"> return False</span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/breakpoint_graph/permutation.py</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/breakpoint_graph/permutation.py</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/breakpoint_graph/permutation.py</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/breakpoint_graph/permutation.py</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/breakpoint_graph/permutation.py</span></span>
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214
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="diff"><span class="p">@@ -118,8 +118,7 @@</span> class PermutationContainer:</span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="diff"> to_keep = target_blocks.intersection(reference_blocks)</span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="diff"> else:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="243" style="width: 35px; color: rgba(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="251" style="width: 35px; color: rgba(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">@@ -243,8 +251,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="diff"> total_length = 0</span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="diff"> total_covered = 0</span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="diff"> for perm in genome_perms:</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;">--- a/ragout/breakpoint_graph/repeat_resolver.py</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/breakpoint_graph/repeat_resolver.py</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/breakpoint_graph/repeat_resolver.py</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/breakpoint_graph/repeat_resolver.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/breakpoint_graph/repeat_resolver.py</span></span>
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248
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="diff"><span class="p">@@ -51,7 +51,7 @@</span> def resolve_repeats(ref_perms, target_pe</span>
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249
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="diff"> next_block_id = 0</span>
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250
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="diff"> for perm in chain(ref_perms, target_perms):</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="410" style="width: 35px; color: rgba(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">@@ -400,19 +410,22 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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400
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="diff"> if block.sign < 0:</span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="diff"> left_context, right_context = (right_context[::-1],</span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/main.py</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/main.py</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/main.py</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/main.py</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/main.py</span></span>
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405
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="diff"><span class="p">@@ -36,10 +36,10 @@</span> from ragout.breakpoint_graph.chimera_det</span>
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406
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="diff"> from ragout.__version__ import __version__</span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="diff"> #register backends</span>
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import synteny_backend.sibelia</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import synteny_backend.sibelia</span></span>
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411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="diff"> #import synteny_backend.cactus</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#import synteny_backend.cactus</span></span>
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412
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423
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import synteny_backend.maf</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import synteny_backend.hal</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;">+from . import synteny_backend.maf</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from . import synteny_backend.hal</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from synteny_backend import sibelia</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#from synteny_backend import cactus</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from synteny_backend import maf</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from synteny_backend import hal</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="diff"> logger = logging.getLogger()</span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="diff"> debugger = DebugConfig.get_instance()</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -425,8 +438,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="diff"> scale = config.vals["blocks"][recipe["blocks"]]</span>
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="diff"> scale = recipe["blocks"]</span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/newick/__init__.py</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/newick/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/newick/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/newick/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/newick/__init__.py</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="diff"><span class="p">@@ -5,14 +5,14 @@</span> Copyright (C) 2003-2008, Thomas Mailund</span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="diff"> '''</span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="diff"> </span>
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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">@@ -447,8 +462,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="diff"> test_suite = unittest.TestSuite()</span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="diff"> test_suite.addTest(lexertest.test_suite)</span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/newick/lexer.py</span></span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/newick/lexer.py</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/newick/lexer.py</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/newick/lexer.py</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/newick/lexer.py</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span> rarely need to access it in your own mod</span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="diff"> use the parser or tree modules, and from those most likely only the</span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="diff"> objects loaded into the mail package. '''</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">@@ -465,8 +482,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from lexertest import test_suite</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from .lexertest import test_suite</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="diff"> unittest.TextTestRunner(verbosity=2).run(test_suite)</span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/newick/lexertest.py</span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/newick/lexertest.py</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/newick/lexertest.py</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/newick/lexertest.py</span></span>
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/newick/lexertest.py</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="diff"> import unittest</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -477,8 +496,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="diff"> class LexerTest(unittest.TestCase):</span>
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="diff"> ''' Test of the Lexer class. '''</span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/newick/parser.py</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/newick/parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/newick/parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/newick/parser.py</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/newick/parser.py</span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="diff"><span class="p">@@ -5,7 +5,7 @@</span> Copyright (C) 2003-2008, Thomas Mailund</span>
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="diff"> </span>
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484
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="diff"> This module contains the functionality for grammatical analysis. '''</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="525" style="width: 35px; color: rgba(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">@@ -504,8 +525,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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504
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from parsertest import test_suite</span></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from .parsertest import test_suite</span></span>
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506
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="diff"> unittest.TextTestRunner(verbosity=2).run(test_suite)</span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/newick/parsertest.py</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/newick/parsertest.py</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/newick/parsertest.py</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/newick/parsertest.py</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/newick/parsertest.py</span></span>
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509
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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510
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="diff"> </span>
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511
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="diff"> import unittest</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -516,8 +539,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="diff"> class ParserTest(unittest.TestCase):</span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="diff"> ''' Test of the _Parser class. '''</span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/newick/tree.py</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/newick/tree.py</span></span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/newick/tree.py</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/newick/tree.py</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/newick/tree.py</span></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="diff"><span class="p">@@ -6,8 +6,8 @@</span> Copyright (C) 2003-2008, Thomas Mailund</span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="diff"> This module contains the representation of trees and a parser for</span>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="diff"> creating trees from a Newick string or file. '''</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">@@ -536,8 +561,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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536
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- from treetest import test_suite</span></span>
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from .treetest import test_suite</span></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="diff"> unittest.TextTestRunner(verbosity=2).run(test_suite)</span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/newick/treetest.py</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/newick/treetest.py</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/newick/treetest.py</span></span>
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/newick/treetest.py</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/newick/treetest.py</span></span>
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541
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="diff"><span class="p">@@ -1,9 +1,9 @@</span></span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="diff"> </span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="diff"> import unittest</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">@@ -552,16 +579,20 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="diff"> </span>
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553
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="diff"> class BuilderTest(unittest.TestCase):</span>
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554
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="diff"> ''' Test of the _TreeBuilder (and Leaf and Tree) class. '''</span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/parsers/phylogeny_parser.py</span></span>
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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/parsers/phylogeny_parser.py</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/parsers/phylogeny_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/parsers/phylogeny_parser.py</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/parsers/phylogeny_parser.py</span></span>
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557
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="diff"><span class="p">@@ -66,4 +66,4 @@</span> def get_leaves_names(newick_str):</span>
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558
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="diff"> if tree is None:</span>
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559
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="diff"> return None</span>
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560
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return list(map(lambda n: n.identifier, tree.get_leaves()))</span></span>
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562
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return list([n.identifier for n in tree.get_leaves()])</span></span>
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563
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/parsers/recipe_parser.py</span></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/parsers/recipe_parser.py</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/parsers/recipe_parser.py</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/parsers/recipe_parser.py</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/parsers/recipe_parser.py</span></span>
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565
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596
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="diff"><span class="p">@@ -72,12 +72,12 @@</span> def parse_ragout_recipe(filename):</span>
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597
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="diff"> if param_name == "blocks":</span>
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567
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="diff"> if value not in config.vals["blocks"]:</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">@@ -588,8 +619,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="diff"> g_params.setdefault(def_key, def_val)</span>
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589
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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="diff"> </span>
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621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="diff"> return recipe_dict</span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/phylogeny/inferer.py</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/phylogeny/inferer.py</span></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/phylogeny/inferer.py</span></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/phylogeny/inferer.py</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/phylogeny/inferer.py</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span> This module infers phylogenetic tree bas</span>
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="diff"> breakpoints data</span>
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="diff"> """</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -608,8 +641,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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641
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="diff"> taxas = list(map(Leaf, sorted(genomes)))</span>
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642
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="diff"> for t in taxas:</span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="diff"> t.terminal = True</span>
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/phylogeny/phylogeny.py</span></span>
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/phylogeny/phylogeny.py</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/phylogeny/phylogeny.py</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/phylogeny/phylogeny.py</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/phylogeny/phylogeny.py</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="diff"><span class="p">@@ -111,7 +111,7 @@</span> class Phylogeny:</span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="diff"> </span>
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="diff"> edges = sorted(root.get_edges(), key=lambda e: e[2], reverse=True)</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">@@ -633,8 +668,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="diff"> </span>
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670
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="diff"> def _median(values):</span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/scaffolder/merge_iters.py</span></span>
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<pre style="margin: 0;">-<span id="LC637" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/scaffolder/merge_iters.py</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/scaffolder/merge_iters.py</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/scaffolder/merge_iters.py</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/scaffolder/merge_iters.py</span></span>
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675
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="diff"><span class="p">@@ -229,10 +229,8 @@</span> class RearrangementProjector:</span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="diff"> new_adj_graph.add_edge(u, v)</span>
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="diff"> </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">@@ -681,8 +718,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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681
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="diff"> link_to_change = left_scf.contigs[left_pos].link</span>
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="diff"> else:</span>
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="diff"> not_found += 1</span>
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684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/scaffolder/output_generator.py</span></span>
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685
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/scaffolder/output_generator.py</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/scaffolder/output_generator.py</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/scaffolder/output_generator.py</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/scaffolder/output_generator.py</span></span>
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686
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="diff"><span class="p">@@ -60,11 +60,11 @@</span> class OutputGenerator:</span>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="diff"> seq_1, seq_2 = get_seq(cnt_1), get_seq(cnt_2)</span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="diff"> </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">@@ -728,8 +767,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="diff"> contigs_n50 = _calc_n50(contigs_len, fragments_len)</span>
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="diff"> scaffolds_n50 = _calc_n50(scaffolds_len, output_len)</span>
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC731" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/scaffolder/scaffolder.py</span></span>
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/scaffolder/scaffolder.py</span></span>
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/scaffolder/scaffolder.py</span></span>
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/scaffolder/scaffolder.py</span></span>
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/scaffolder/scaffolder.py</span></span>
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="diff"><span class="p">@@ -35,7 +35,7 @@</span> def build_scaffolds(adjacencies, perm_co</span>
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="diff"> contigs, contig_index = _make_contigs(perm_container)</span>
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="diff"> scaffolds = _extend_scaffolds(adjacencies, contigs, contig_index,</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">@@ -762,8 +803,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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762
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="diff"> new_contigs[i].link = new_contigs[i + 1].link</span>
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="diff"> new_contigs[-1].link = Link(0, [])</span>
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="diff"> scf.contigs = new_contigs</span>
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/shared/datatypes.py</span></span>
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/shared/datatypes.py</span></span>
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/shared/datatypes.py</span></span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/shared/datatypes.py</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/shared/datatypes.py</span></span>
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="diff"><span class="p">@@ -63,7 +63,7 @@</span> class Permutation:</span>
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768
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="diff"> def __str__(self):</span>
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769
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="diff"> return ("[{0}, {1}, {2}, b:{3}, e:{4}]"</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -785,8 +828,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="diff"> </span>
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786
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="diff"> def name(self):</span>
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787
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="diff"> return self.perm.name()</span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/synteny_backend/cactus.py</span></span>
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789
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<pre style="margin: 0;">-<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/synteny_backend/cactus.py</span></span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/synteny_backend/cactus.py</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/synteny_backend/cactus.py</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/synteny_backend/cactus.py</span></span>
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790
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="diff"><span class="p">@@ -64,7 +64,7 @@</span> def _make_permutations(recipe, output_di</span>
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="diff"> </span>
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792
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="diff"> else:</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="850" style="width: 35px; color: rgba(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">@@ -805,8 +850,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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805
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="diff"> if genome != recipe["target"]:</span>
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806
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="diff"> file.write("*")</span>
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807
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="diff"> file.write("{0} {1}\n".format(genome, os.path.abspath(params["fasta"])))</span>
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808
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/synteny_backend/sibelia.py</span></span>
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809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/synteny_backend/sibelia.py</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/ragout/synteny_backend/sibelia.py</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/ragout/synteny_backend/sibelia.py</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/ragout/synteny_backend/sibelia.py</span></span>
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810
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<td class="diff-line-num new_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="diff"><span class="p">@@ -70,7 +70,7 @@</span> class SibeliaBackend(SyntenyBackend):</span>
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811
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<td class="diff-line-num new_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="diff"> if not os.path.isdir(block_dir):</span>
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812
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="diff"> os.mkdir(block_dir)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="872" style="width: 35px; color: rgba(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">@@ -825,8 +872,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<td class="diff-line-num old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
825
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="diff"> if "fasta" not in gen_params:</span>
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<td class="diff-line-num old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
826
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<td class="diff-line-num new_line" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="diff"> raise BackendException("FASTA file for '{0}' is not "</span>
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<td class="diff-line-num old_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
827
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="diff"> "specified".format(gen_name))</span>
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828
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/2geneorder.py</span></span>
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829
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/2geneorder.py</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/2geneorder.py</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/2geneorder.py</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/2geneorder.py</span></span>
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830
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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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831
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<td class="diff-line-num old_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
832
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<td class="diff-line-num new_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -851,8 +900,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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851
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="diff"> print(">{0}".format(genome))</span>
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852
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="diff"> for seq in seqs:</span>
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853
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="diff"> print(seq)</span>
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854
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<pre style="margin: 0;">-<span id="LC854" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/compare-assemblies.py</span></span>
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855
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<pre style="margin: 0;">-<span id="LC855" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/compare-assemblies.py</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/compare-assemblies.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/compare-assemblies.py</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/compare-assemblies.py</span></span>
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856
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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857
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>
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858
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="958" style="width: 35px; color: rgba(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">@@ -907,8 +958,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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907
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="diff"> for block_1, block_2 in zip(blocks[:-1], blocks[1:]):</span>
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908
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="diff"> graph.add_edge(-block_1, block_2, name=seq, color="green")</span>
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909
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="diff"> </span>
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910
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/debug-report.py</span></span>
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911
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/debug-report.py</span></span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/debug-report.py</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/debug-report.py</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/debug-report.py</span></span>
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912
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num old_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
913
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>
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<td class="diff-line-num old_line" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
914
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -975,8 +1028,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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975
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="diff"> #alignment = join_collinear(alignment)</span>
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976
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<td class="diff-line-num new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="diff"> alignment = filter_by_coverage(alignment, 0.7)</span>
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<td class="diff-line-num old_line" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
977
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1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="diff"> alignment = join_collinear(alignment)</span>
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978
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<td class="diff-line-num new_line old" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC978" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/install-sibelia.py</span></span>
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979
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/install-sibelia.py</span></span>
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1031
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<pre style="margin: 0;">+<span id="LC1031" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/install-sibelia.py</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/install-sibelia.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/install-sibelia.py</span></span>
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980
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1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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981
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<td class="diff-line-num new_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num old_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
982
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<td class="diff-line-num new_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="999" style="width: 35px; color: rgba(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="1054" style="width: 35px; color: rgba(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">@@ -999,8 +1054,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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999
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<td class="diff-line-num new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="diff"> except ImportError:</span>
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1000
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<td class="diff-line-num new_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="diff"> from urllib.request import urlretrieve</span>
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<td class="diff-line-num old_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1001
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="diff"> </span>
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1002
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<td class="diff-line-num new_line old" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/run-tests.py</span></span>
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1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/run-tests.py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/run-tests.py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1058
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/run-tests.py</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/run-tests.py</span></span>
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<td class="diff-line-num old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1004
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<td class="diff-line-num new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num old_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1005
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<td class="diff-line-num new_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1062
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>
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<td class="diff-line-num old_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1006
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<td class="diff-line-num new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1025" style="width: 35px; color: rgba(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="1082" style="width: 35px; color: rgba(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">@@ -1025,8 +1082,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<td class="diff-line-num old_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1025
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1082
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="diff"> print("\n********Running test:", name, "********\n")</span>
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<td class="diff-line-num old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1026
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<td class="diff-line-num new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="diff"> run_test(params)</span>
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<td class="diff-line-num old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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<td class="diff-line-num new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="diff"> </span>
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<td class="diff-line-num old old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1028
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<td class="diff-line-num new_line old" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1028" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/simulate-rearrangements.py</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1029
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<td class="diff-line-num new_line old" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1029" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/simulate-rearrangements.py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/simulate-rearrangements.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/simulate-rearrangements.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/simulate-rearrangements.py</span></span>
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1030
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<td class="diff-line-num new_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num old_line" data-linenumber="1031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1031
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<td class="diff-line-num new_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>
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<td class="diff-line-num old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1032
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<td class="diff-line-num new_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1051" style="width: 35px; color: rgba(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="1110" style="width: 35px; color: rgba(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">@@ -1051,8 +1110,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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1051
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1110
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<pre style="margin: 0;"> <span id="LC1110" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1052
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<td class="diff-line-num new_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="diff"> unique_seq.remove(contig)</span>
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<td class="diff-line-num old_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1053
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<td class="diff-line-num new_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="diff"> if not unique_seq:</span>
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<td class="diff-line-num old old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1054
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<td class="diff-line-num new_line old" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1054" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/utils/common.py</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1055
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<td class="diff-line-num new_line old" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1055" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/utils/common.py</span></span>
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1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/utils/common.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/utils/common.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/utils/common.py</span></span>
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1056
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<td class="diff-line-num new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="diff"><span class="p">@@ -89,7 +89,7 @@</span> def filter_by_coverage(alignment, thresh</span>
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1057
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<td class="diff-line-num new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="diff"> by_name[name] = list(filter(len_filter, by_name[name]))</span>
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<td class="diff-line-num old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1058
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<td class="diff-line-num new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1071" style="width: 35px; color: rgba(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="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1071,8 +1132,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<td class="diff-line-num old_line" data-linenumber="1071" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1071
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<td class="diff-line-num new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="diff"> for e in alignment:</span>
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<td class="diff-line-num old_line" data-linenumber="1072" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1072
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<td class="diff-line-num new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="diff"> if prev_start is not None and e.ref.start > prev_start:</span>
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<td class="diff-line-num old_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1073
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="diff"> contig_pos += 1</span>
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<td class="diff-line-num old old_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1074
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<td class="diff-line-num new_line old" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1074" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/utils/lastz_parser.py</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1075
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<td class="diff-line-num new_line old" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1075" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/utils/lastz_parser.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1135
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<pre style="margin: 0;">+<span id="LC1135" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/utils/lastz_parser.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/utils/lastz_parser.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/utils/lastz_parser.py</span></span>
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1076
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<td class="diff-line-num new_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="diff"><span class="p">@@ -68,8 +68,8 @@</span> def filter_intersecting(alignments):</span>
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<td class="diff-line-num old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1077
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<td class="diff-line-num new_line" data-linenumber="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="diff"> if not (row_2.start <= row_1.end <= row_2.end):</span>
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<td class="diff-line-num old_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1078
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<td class="diff-line-num new_line" data-linenumber="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1141
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<pre style="margin: 0;"> <span id="LC1141" class="line" lang="diff"> to_filter.add(row_2)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1084" style="width: 35px; color: rgba(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="1147" style="width: 35px; color: rgba(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">@@ -1084,8 +1147,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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1084
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1147
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<pre style="margin: 0;"> <span id="LC1147" class="line" lang="diff"> </span>
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1085
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<td class="diff-line-num new_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1148
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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="diff"> return [a for a in alignments if a.ref not in to_filter and</span>
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<td class="diff-line-num old_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1086
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<td class="diff-line-num new_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="diff"> a.qry not in to_filter]</span>
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<td class="diff-line-num old old_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1087
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<td class="diff-line-num new_line old" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1087" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/verify-minimap.py</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1088
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<td class="diff-line-num new_line old" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1088" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/verify-minimap.py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/verify-minimap.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/verify-minimap.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/verify-minimap.py</span></span>
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1089
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<td class="diff-line-num new_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1154
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num old_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1090
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<td class="diff-line-num new_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>
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<td class="diff-line-num old_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1091
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<td class="diff-line-num new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1184" style="width: 35px; color: rgba(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">@@ -1119,8 +1184,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<td class="diff-line-num old_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1119
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<td class="diff-line-num new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="diff"> if not miss_ord and prev_strand and cur_strand:</span>
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<td class="diff-line-num old_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1120
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<td class="diff-line-num new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1185
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1185" class="line" lang="diff"> if not agreement_strands(prev_strand, cur_strand, increasing):</span>
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<td class="diff-line-num old_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1121
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<td class="diff-line-num new_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="diff"> breaks.append(contig.name)</span>
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<td class="diff-line-num old old_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1122
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<td class="diff-line-num new_line old" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/verify-order.py</span></span>
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1123
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<td class="diff-line-num new_line old" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/verify-order.py</span></span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/scripts/verify-order.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/scripts/verify-order.py</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/scripts/verify-order.py</span></span>
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1124
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<td class="diff-line-num new_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1191
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<pre style="margin: 0;"> <span id="LC1191" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num old_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1125
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<td class="diff-line-num new_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1192
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<pre style="margin: 0;"> <span id="LC1192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>
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<td class="diff-line-num old_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1126
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<td class="diff-line-num new_line" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1193
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<pre style="margin: 0;"> <span id="LC1193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1146" style="width: 35px; color: rgba(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="1213" style="width: 35px; color: rgba(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">@@ -1146,8 +1213,10 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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<td class="diff-line-num old_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1146
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<td class="diff-line-num new_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="diff"> if not miss_ord and prev_strand and cur_strand:</span>
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<td class="diff-line-num old_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1147
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<td class="diff-line-num new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="diff"> if not agreement_strands(prev_strand, cur_strand, increasing):</span>
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<td class="diff-line-num old_line" data-linenumber="1148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1148
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<td class="diff-line-num new_line" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1215
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="diff"> breaks.append(contig.name)</span>
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<td class="diff-line-num old old_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1149
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<td class="diff-line-num new_line old" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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1150
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<pre style="margin: 0;">-<span id="LC1150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/setup.py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); 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="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/setup.py</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); 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="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/setup.py</span></span>
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1151
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<td class="diff-line-num new_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="diff"><span class="p">@@ -2,14 +2,14 @@</span></span>
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<td class="diff-line-num old_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1152
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<td class="diff-line-num new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="diff"> #This file is a part of Ragout program.</span>
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<td class="diff-line-num old_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1153
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<td class="diff-line-num new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="diff"> #Released under the BSD license (see LICENSE file)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1168" style="width: 35px; color: rgba(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="1237" style="width: 35px; color: rgba(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">@@ -1168,3 +1237,35 @@ Reported upstream in: https://github.com/fenderglass/Ragout/issues/52</td>
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1168
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<td class="diff-line-num new_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1237
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<pre style="margin: 0;"> <span id="LC1237" class="line" lang="diff"> </span>
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<td class="diff-line-num old_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1169
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<td class="diff-line-num new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1238
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<pre style="margin: 0;"> <span id="LC1238" class="line" lang="diff"> from distutils.core import setup</span>
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<td class="diff-line-num old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1170
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<td class="diff-line-num new_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1239
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<pre style="margin: 0;"> <span id="LC1239" class="line" lang="diff"> from distutils.command.build import build as DistutilsBuild</span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/bin/ragout</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/bin/ragout</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/bin/ragout</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1244
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<pre style="margin: 0;">+<span id="LC1244" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1245
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<pre style="margin: 0;">+<span id="LC1245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python2.7</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="diff"> #(c) 2013-2014 by Authors</span>
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<td class="diff-line-num new new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1249
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<pre style="margin: 0;">+<span id="LC1249" class="line" lang="diff"> #This file is a part of Ragout program.</span>
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<td class="diff-line-num new new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="diff"><span class="p">@@ -12,21 +12,6 @@</span> and invokes Ragout</span>
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1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="diff"> import os</span>
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1252
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<pre style="margin: 0;">+<span id="LC1252" class="line" lang="diff"> import sys</span>
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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="diff"> </span>
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1254
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<pre style="margin: 0;">+<span id="LC1254" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-BIN_DIR = "bin"</span></span>
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1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#Check Python version</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-if sys.version_info[:2] != (2, 7):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print("Error: Ragout requires Python version 2.7 ({0}.{1} detected)."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .format(sys.version_info[0], sys.version_info[1]))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sys.exit(-1)</span></span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#Setting executable paths</span></span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-ragout_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))</span></span>
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<pre style="margin: 0;">+<span id="LC1264" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-sys.path.insert(0, ragout_root)</span></span>
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bin_absolute = os.path.join(ragout_root, BIN_DIR)</span></span>
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1267
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<pre style="margin: 0;">+<span id="LC1267" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-os.environ["PATH"] = bin_absolute + os.pathsep + os.environ["PATH"]</span></span>
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1268
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<pre style="margin: 0;">+<span id="LC1268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC1269" class="line" lang="diff"> #Ragout entry point</span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="diff"> from ragout.main import main</span>
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1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="diff"> sys.exit(main())</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61#49cce42d8923c0f68a3e48ad8f9039dfa5479cee"><strong>debian/patches/adjustSetupParsingBinaries.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: ragout/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ragout.orig/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ragout/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -39,6 +39,6 @@</span> setup(name='ragout',</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> 'ragout/phylogeny', 'ragout/scaffolder', 'ragout/shared',</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> 'ragout/synteny_backend', 'ragout/newick'],</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> package_data={'ragout': ['LICENSE']},</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- scripts = ['bin/ragout-maf2synteny', 'bin/ragout-overlap', 'bin/ragout'],</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #scripts = ['bin/ragout-maf2synteny', 'bin/ragout-overlap', 'bin/ragout'],</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> cmdclass={'build': MakeBuild}</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> )</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61#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>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">adjustSetupParsingBinaries.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61#5eaab3a6d332a70f8f7ab5b488590b063dc6f4c8"><strong>debian/ragout.install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="php"><span class="nx">usr</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">bin</span><span class="o" style="font-weight: 600;">/</span><span class="nx">ragout</span><span class="o" style="font-weight: 600;">*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/commit/c8991daa17bb287539836c822f77dfe48368fe61#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,3 +13,9 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> find debian -name LICENSE -delete</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> rm -f bin/ragout-maf2synteny bin/ragout-overlap</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> rm -rf .pybuild</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> find . -name "*.o" -delete</span></pre>
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