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<h3>
Andreas Tille 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/76c27fffc79ca6419fb41b73a5d04ae219588583">76c27fff</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-03-26T10:51:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt to python-networkx >= 2 (Thanks a lot to Tatiana Malygina <merlettaia@gmail.com> for the patches)
</pre>
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<strong><a href="https://salsa.debian.org/med-team/ragout/commit/12f1dde8dd02069244aa52de0301ec180c09af98">12f1dde8</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-03-26T10:52:35Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Versioned (Build-)Depends python-networkx (since now this fails for version 1.x)
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#cb9ce3db83bd991ab16e3244af73fdbb05cadc6b">
<span class="new-file">
+
debian/patches/d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch
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</li>
<li class="file-stats">
<a href="#c31b425c1dd1fb15d86e40bfd7f75b939ec86628">
<span class="new-file">
+
debian/patches/e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch
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</li>
<li class="file-stats">
<a href="#8194198ebc7d60a0d46fd726e66ad61bc88dd5b6">
<span class="new-file">
+
debian/patches/f4d4e2223a337abdbc5873fd6560e1494e55342d.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/ragout/compare/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6...12f1dde8dd02069244aa52de0301ec180c09af98#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,7 +6,7 @@ Priority: optional</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python-dev,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> python-networkx</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python-networkx<span class="idiff left right"> (>= 2.2)</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/ragout</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/ragout.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${python:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<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="LC21" class="line" lang="plaintext"> python-networkx</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python-networkx<span class="idiff left right"> (>= 2.2)</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Description: Reference-Assisted Genome Ordering UTility</span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> Ragout (Reference-Assisted Genome Ordering UTility) is a tool for</span>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" 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/compare/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6...12f1dde8dd02069244aa52de0301ec180c09af98#cb9ce3db83bd991ab16e3244af73fdbb05cadc6b"><strong>debian/patches/d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0 Mon Sep 17 00:00:00 2001</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">From: Tatiana Malygina <merlettaia@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Date: Mon, 25 Mar 2019 16:09:21 +0300</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Origin: https://github.com/fenderglass/Ragout/pull/41</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Subject: [PATCH] replace edges_iter iterator with edges iterator in networkx</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> graphs</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">---</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> ragout/breakpoint_graph/breakpoint_graph.py | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> ragout/breakpoint_graph/chimera_detector.py | 2 +-</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> ragout/breakpoint_graph/inferer.py | 4 ++--</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> ragout/scaffolder/merge_iters.py | 4 ++--</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> scripts/debug-report.py | 6 +++---</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 5 files changed, 9 insertions(+), 9 deletions(-)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ragout/breakpoint_graph/breakpoint_graph.py b/ragout/breakpoint_graph/breakpoint_graph.py</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gh" style="color: #999;">index c9aa6c2..e73afd9 100644</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" 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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19
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<pre style="margin: 0;">+<span id="LC19" 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="LC20" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -272,7 +272,7 @@ def _output_graph(graph, out_file):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> with open(out_file, "w") as fout:</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> fout.write("graph {\n")</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2, data in graph.edges_iter(data=True):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2, data in graph.edges(data=True):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> fout.write("{0} -- {1}".format(v1, v2))</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> if len(data):</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> extra = list(map(lambda (k, v) : "{0}=\"{1}\"".format(k, v),</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ragout/breakpoint_graph/chimera_detector.py b/ragout/breakpoint_graph/chimera_detector.py</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gh" style="color: #999;">index d72440f..06b8f08 100644</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/breakpoint_graph/chimera_detector.py</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" 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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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -98,7 +98,7 @@ def _get_contig_breaks(self, bp_graph):</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> logger.debug("Processing component of size {0}"</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> .format(len(subgr.bp_graph)))</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (u, v, data) in subgr.bp_graph.edges_iter(data=True):</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (u, v, data) in subgr.bp_graph.edges(data=True):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> if data["genome_id"] != subgr.target:</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> continue</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ragout/breakpoint_graph/inferer.py b/ragout/breakpoint_graph/inferer.py</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gh" style="color: #999;">index a2c8134..7cdc5c3 100644</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/breakpoint_graph/inferer.py</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/breakpoint_graph/inferer.py</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -115,7 +115,7 @@ def _trim_known_edges(self, graph):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> Removes edges with known target adjacencies (red edges from paper)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> trimmed_graph = graph.copy()</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2 in graph.edges_iter():</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2 in graph.edges():</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> if not trimmed_graph.has_node(v1) or not trimmed_graph.has_node(v2):</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> continue</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -142,7 +142,7 @@ def _min_weight_matching(graph):</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> Finds a perfect matching with minimum weight</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> """</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2 in graph.edges_iter():</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2 in graph.edges():</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> graph[v1][v2]["weight"] = -graph[v1][v2]["weight"] #want minimum weght</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> MIN_LOG_SIZE = 20</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ragout/scaffolder/merge_iters.py b/ragout/scaffolder/merge_iters.py</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gh" style="color: #999;">index fd6c9cd..66be623 100644</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/scaffolder/merge_iters.py</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/scaffolder/merge_iters.py</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -179,7 +179,7 @@ def project(self):</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> red_edges = []</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> black_edges = []</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (u, v, data) in subgr.edges_iter(data=True):</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (u, v, data) in subgr.edges(data=True):</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> if data["scf_set"] == "old":</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> red_edges.append((u, v))</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -201,7 +201,7 @@ def project(self):</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> logger.debug("Made {0} k-breaks".format(num_kbreaks))</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> adjacencies = {}</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (u, v, data) in self.bp_graph.edges_iter(data=True):</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (u, v, data) in self.bp_graph.edges(data=True):</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> if data["scf_set"] == "old":</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> gap, support = 0, []</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> if not data["infinity"]:</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/scripts/debug-report.py b/scripts/debug-report.py</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gh" style="color: #999;">index 017d3c8..e118f46 100755</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/debug-report.py</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/debug-report.py</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -113,11 +113,11 @@ def compose_breakpoint_graph(base_dot, predicted_dot, true_edges):</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> predicted_edges = nx.read_dot(predicted_dot)</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> out_graph = nx.MultiGraph()</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2, data in base_graph.edges_iter(data=True):</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2, data in base_graph.edges(data=True):</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> color = g2c(data["genome_id"])</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> label = "oo" if data["infinity"] == "True" else ""</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> out_graph.add_edge(v1, v2, color=color, label=label)</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2 in predicted_edges.edges_iter():</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2 in predicted_edges.edges():</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> out_graph.add_edge(v1, v2, color="red", style="dashed")</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> for (v1, v2, infinite) in true_edges:</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> label = "oo" if infinite else ""</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -140,7 +140,7 @@ def output_graph(graph, output_dir, only_predicted):</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> if only_predicted:</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> to_show = False</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2, data in subgr.edges_iter(data=True):</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2, data in subgr.edges(data=True):</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> if data.get("style") == "dashed":</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> to_show = True</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> break</span></pre>
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<li id="c31b425c1dd1fb15d86e40bfd7f75b939ec86628">
<a href="https://salsa.debian.org/med-team/ragout/compare/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6...12f1dde8dd02069244aa52de0301ec180c09af98#c31b425c1dd1fb15d86e40bfd7f75b939ec86628"><strong>debian/patches/e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From e3a06ef1256cf132903bbf19c9d4e11ea846e6df Mon Sep 17 00:00:00 2001</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">From: Tatiana Malygina <merlettaia@gmail.com></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Date: Mon, 25 Mar 2019 16:19:40 +0300</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Origin: https://github.com/fenderglass/Ragout/pull/41</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Subject: [PATCH] fix TypeError: object of type 'dictionary-keyiterator' has no</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> len()</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">---</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> ragout/scaffolder/merge_iters.py | 3 ++-</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> 1 file changed, 2 insertions(+), 1 deletion(-)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ragout/scaffolder/merge_iters.py b/ragout/scaffolder/merge_iters.py</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gh" style="color: #999;">index 66be623..3536f5c 100644</span></span>
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<pre style="margin: 0;">+<span id="LC14" 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="LC15" 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="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -174,7 +174,7 @@ def project(self):</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> subgraphs = list(nx.connected_component_subgraphs(self.bp_graph))</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> for subgr in subgraphs:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> #this is a cycle</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if any(len(subgr.neighbors(node)) != 2 for node in subgr.nodes()):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if any(len(subgr[node]) != 2 for node in subgr.nodes()):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> continue</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> red_edges = []</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -193,6 +193,7 @@ def project(self):</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> self.bp_graph.remove_edge(u, v)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> self.adj_graph.remove_edge(u, v)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> for u, v in black_edges:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(self.bp_graph[u][v])</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> link = self.bp_graph[u][v][0]["link"]</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> infinity = self.bp_graph[u][v][0]["infinity"]</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> self.bp_graph.add_edge(u, v, scf_set="old",</span></pre>
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<li id="8194198ebc7d60a0d46fd726e66ad61bc88dd5b6">
<a href="https://salsa.debian.org/med-team/ragout/compare/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6...12f1dde8dd02069244aa52de0301ec180c09af98#8194198ebc7d60a0d46fd726e66ad61bc88dd5b6"><strong>debian/patches/f4d4e2223a337abdbc5873fd6560e1494e55342d.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">From f4d4e2223a337abdbc5873fd6560e1494e55342d Mon Sep 17 00:00:00 2001</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">From: Tatiana Malygina <merlettaia@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Date: Mon, 25 Mar 2019 17:08:08 +0300</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Origin: https://github.com/fenderglass/Ragout/pull/41</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Subject: [PATCH] fix AttributeError: 'set' object has no attribute 'items'</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">---</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ragout/breakpoint_graph/inferer.py | 2 +-</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> ragout/breakpoint_graph/repeat_resolver.py | 2 +-</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> 2 files changed, 2 insertions(+), 2 deletions(-)</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ragout/breakpoint_graph/inferer.py b/ragout/breakpoint_graph/inferer.py</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gh" style="color: #999;">index 7cdc5c3..eb47032 100644</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/ragout/breakpoint_graph/inferer.py</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/ragout/breakpoint_graph/inferer.py</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -151,7 +151,7 @@ def _min_weight_matching(graph):</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> "size {0}".format(len(graph)))</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> edges = nx.max_weight_matching(graph, maxcardinality=True)</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> unique_edges = set()</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2 in edges.items():</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2 in edges:</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> if not (v2, v1) in unique_edges:</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> unique_edges.add((v1, v2))</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/ragout/breakpoint_graph/repeat_resolver.py b/ragout/breakpoint_graph/repeat_resolver.py</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gh" style="color: #999;">index b3054e5..a20ea11 100644</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" 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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28
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<pre style="margin: 0;">+<span id="LC28" 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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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -362,7 +362,7 @@ def _profile_similarity(profile, genome_ctx, repeats, same_len):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> def _max_weight_matching(graph):</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> edges = nx.max_weight_matching(graph, maxcardinality=True)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> unique_edges = set()</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for v1, v2 in edges.items():</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for v1, v2 in edges:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> if not (v2, v1) in unique_edges:</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> unique_edges.add((v1, v2))</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/ragout/compare/b1fcb230f6b4dc696c1d4aa8111f0a625024aab6...12f1dde8dd02069244aa52de0301ec180c09af98#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">install_newick.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">d49a5c46f73c1a4a2bfcbf5bbe41b9d2dab5f5f0.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">e3a06ef1256cf132903bbf19c9d4e11ea846e6df.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">f4d4e2223a337abdbc5873fd6560e1494e55342d.patch</span></pre>
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