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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/unicycler">Debian Med / unicycler</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb">2c389812</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-11-12T15:01:57Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.4.8+dfsg</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#e07e4f4df25ef64edebe3ab13cd08a9fef3375e2">
unicycler/assembly_graph.py
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<li class="file-stats">
<a href="#517cc28b7cbb91d9c10dc74557348d3a352580bd">
unicycler/bridge_long_read_simple.py
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<li class="file-stats">
<a href="#6485221094e804d80f1086ea211fb69e2c82f8aa">
unicycler/settings.py
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<li class="file-stats">
<a href="#1f941b6b2d8d60232d459f825127d673bce10b87">
unicycler/spades_func.py
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<li class="file-stats">
<a href="#e7416bd43296684326192cb201ec8dcbd20ab982">
unicycler/src/miniasm/hit.cpp
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<li class="file-stats">
<a href="#59fca07fac6fd9e5a326c480accace22111a2286">
unicycler/unicycler.py
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<li class="file-stats">
<a href="#4ca27ed8dd1770540001efbc5ee5a9cce34f7366">
unicycler/version.py
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -428,6 +428,8 @@ SPAdes assembly:</td>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="markdown"> --depth_filter DEPTH_FILTER Filter out contigs lower than this fraction of the chromosomal</span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="markdown"> depth, if doing so does not result in graph dead ends (default:</span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="markdown"> 0.25)</span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="markdown"> --largest_component Only keep the largest connected component of the assembly graph</span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="markdown"> (default: keep all connected components)</span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="markdown"> --spades_tmp_dir SPADES_TMP_DIR</span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="markdown"> Specify SPAdes temporary directory using the SPAdes --tmp-dir</span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="markdown"> option (default: make a temporary directory in the output</span>
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<li id="e07e4f4df25ef64edebe3ab13cd08a9fef3375e2">
<a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb#e07e4f4df25ef64edebe3ab13cd08a9fef3375e2"><strong>unicycler/assembly_graph.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -423,6 +423,7 @@ class AssemblyGraph(object):</td>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"><span class="s" style="color: #d14;"> 3) deleting the segment would not create any dead ends</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">segment_nums_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">total_length_removed</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">ten_longest_contigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">segments</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">(),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_length</span><span class="p">())[:</span><span class="mi" style="color: #099;">10</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">whole_graph_cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_median_read_depth</span><span class="p">(</span><span class="n" style="color: #333;">ten_longest_contigs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">relative_depth_cutoff</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -437,7 +438,9 @@ class AssemblyGraph(object):</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">all_segments_below_depth</span><span class="p">(</span><span class="n" style="color: #333;">component</span><span class="p">,</span> <span class="n" style="color: #333;">whole_graph_cutoff</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dead_end_change_if_deleted</span><span class="p">(</span><span class="n" style="color: #333;">seg_num</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"> <span class="n" style="color: #333;">segment_nums_to_remove</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seg_num</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">total_length_removed</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">segment</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_length</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove_segments</span><span class="p">(</span><span class="n" style="color: #333;">segment_nums_to_remove</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">segment_nums_to_remove</span><span class="p">),</span> <span class="n" style="color: #333;">total_length_removed</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filter_homopolymer_loops</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -455,6 +458,28 @@ class AssemblyGraph(object):</td>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Removed homopolymer loops:'</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_number_list</span><span class="p">(</span><span class="n" style="color: #333;">segment_nums_to_remove</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">choose_largest_component</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"><span class="s" style="color: #d14;"> Special logic: throw out all of the graph's connected components except for the largest one.</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">largest_component_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">connected_components</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_connected_components</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">component_nums</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">connected_components</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">component_segments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">segments</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">component_nums</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">component_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_length</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">component_segments</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">largest_component_length</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">component_length</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">largest_component_length</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">largest_component_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">component_length</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="python"> <span class="n" style="color: #333;">segment_nums_to_remove</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">component_nums</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">connected_components</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">component_segments</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">segments</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">component_nums</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">component_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_length</span><span class="p">()</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">component_segments</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">component_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">largest_component_length</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">segment_nums_to_remove</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">component_nums</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove_segments</span><span class="p">(</span><span class="n" style="color: #333;">segment_nums_to_remove</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">segment_nums_to_remove</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Removed not-largest components:'</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_number_list</span><span class="p">(</span><span class="n" style="color: #333;">segment_nums_to_remove</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remove_segments</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">nums_to_remove</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"><span class="s" style="color: #d14;"> This function deletes all segments in the nums_to_remove list, along with their links. It</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -923,7 +948,7 @@ class AssemblyGraph(object):</td>
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="python"> <span class="n" style="color: #333;">dead_ends</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC949" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">potential_dead_ends</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dead_ends</span></span>
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<pre style="margin: 0;"> <span id="LC950" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC926" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read_depth_filter</span><span class="p">):</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read_depth_filter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">largest_component</span></span><span class="p">):</span></span>
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927
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952
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<pre style="margin: 0;"> <span id="LC952" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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928
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="python"><span class="s" style="color: #d14;"> This function does various graph repairs, filters and normalisations to make it a bit</span></span>
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929
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954
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="python"><span class="s" style="color: #d14;"> nicer.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); 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="956" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -931,9 +956,12 @@ class AssemblyGraph(object):</td>
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Repair multi way junctions '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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932
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">repair_multi_way_junctions</span><span class="p">()</span></span>
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933
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958
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<pre style="margin: 0;"> <span id="LC958" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Filter by read depth '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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934
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter_by_read_depth</span><span class="p">(</span><span class="n" style="color: #333;">read_depth_filter</span><span class="p">)</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">removed_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">removed_length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter_by_read_depth</span><span class="p">(</span><span class="n" style="color: #333;">read_depth_filter</span><span class="p">)</span></span>
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935
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Filter homopolymer loops '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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936
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter_homopolymer_loops</span><span class="p">()</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">largest_component</span><span class="p">:</span></span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Keep largest component '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">choose_largest_component</span><span class="p">()</span></span>
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937
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Merge all possible '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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938
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966
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<pre style="margin: 0;"> <span id="LC966" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">merge_all_possible</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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939
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967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Normalise read depths '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -943,6 +971,7 @@ class AssemblyGraph(object):</td>
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943
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971
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Sort link order '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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944
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972
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort_link_order</span><span class="p">()</span></span>
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945
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Graph cleaning finished '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_dim_timestamp</span><span class="p">(),</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">removed_count</span><span class="p">,</span> <span class="n" style="color: #333;">removed_length</span></span>
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC976" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">final_clean</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC977" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb#517cc28b7cbb91d9c10dc74557348d3a352580bd"><strong>unicycler/bridge_long_read_simple.py</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">@@ -490,7 +490,7 @@ def get_read_loop_vote(start, end, middle, repeat, strand, minimap_alignments, r</td>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"> <span class="n" style="color: #333;">best_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">test_seq_score</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">best_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loop_count</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Break when we've hit the max loop count. But if the max is<span class="idiff left right">n't</span> our best, then we keep</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Break when we've hit the max loop count. But if the max is our best, then we keep</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># trying higher.</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">loop_count</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">max_tested_loop_count</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">loop_count</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">best_count</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb#6485221094e804d80f1086ea211fb69e2c82f8aa"><strong>unicycler/settings.py</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">@@ -30,8 +30,8 @@ SIMPLE_REPEAT_BRIDGING_BAND_SIZE = 50</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">CONTIG_READ_QSCORE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">40</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This is the maximum number of times an assembly will be Racon polished</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">RACON_POLISH_LOOP_COUNT_HYBRID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"><span class="n" style="color: #333;">RACON_POLISH_LOOP_COUNT_LONG_ONLY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">10</span></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">RACON_POLISH_LOOP_COUNT_HYBRID</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="n" style="color: #333;">RACON_POLISH_LOOP_COUNT_LONG_ONLY</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This is the number of times assembly graph contigs are included in the Racon polish reads. E.g.</span></span>
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<a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb#1f941b6b2d8d60232d459f825127d673bce10b87"><strong>unicycler/spades_func.py</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">@@ -30,7 +30,8 @@ class BadFastq(Exception):</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_best_spades_graph</span><span class="p">(</span><span class="n" style="color: #333;">short1</span><span class="p">,</span> <span class="n" style="color: #333;">short2</span><span class="p">,</span> <span class="n" style="color: #333;">short_unpaired</span><span class="p">,</span> <span class="n" style="color: #333;">out_dir</span><span class="p">,</span> <span class="n" style="color: #333;">read_depth_filter</span><span class="p">,</span> <span class="n" style="color: #333;">verbosity</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">spades_path</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">keep</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_count</span><span class="p">,</span> <span class="n" style="color: #333;">min_k_frac</span><span class="p">,</span> <span class="n" style="color: #333;">max_k_frac</span><span class="p">,</span> <span class="n" style="color: #333;">kmers</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">no_spades_correct</span><span class="p">,</span> <span class="n" style="color: #333;">expected_linear_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">spades_tmp_dir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">no_spades_correct</span><span class="p">,</span> <span class="n" style="color: #333;">expected_linear_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">spades_tmp_dir</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">largest_component</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> This function tries a SPAdes assembly at different k-mers and returns the best.</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> 'The best' is defined as the smallest dead-end count after low-depth filtering. If multiple</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,7 +127,7 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Cleaning k{} graph'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">assembly_graph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clean</span><span class="p">(</span><span class="n" style="color: #333;">read_depth_filter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">assembly_graph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clean</span><span class="p">(</span><span class="n" style="color: #333;">read_depth_filter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">largest_component</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">clean_graph_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">spades_dir</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">'k</span><span class="si" style="color: #d14;">%03</span><span class="s" style="color: #d14;">d'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_assembly_graph.gfa'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">assembly_graph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">save_to_gfa</span><span class="p">(</span><span class="n" style="color: #333;">clean_graph_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbosity</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></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">@@ -183,7 +184,7 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi</td>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">assembly_graph</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AssemblyGraph</span><span class="p">(</span><span class="n" style="color: #333;">best_graph_filename</span><span class="p">,</span> <span class="n" style="color: #333;">best_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">paths_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">paths_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">insert_size_mean</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">insert_size_mean</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">insert_size_deviation</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">insert_size_deviation</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">assembly_graph</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">clean</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">read_depth_filter</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">removed_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">removed_length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">assembly_graph</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">clean</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read_depth_filter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">largest_component</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">clean_graph_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">spades_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'k'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">best_kmer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_assembly_graph.gfa'</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">assembly_graph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">save_to_gfa</span><span class="p">(</span><span class="n" style="color: #333;">clean_graph_filename</span><span class="p">,</span> <span class="n" style="color: #333;">verbosity</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"></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">@@ -197,9 +198,14 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi</td>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">row_colour</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="n" style="color: #333;">best_kmer_row</span><span class="p">:</span> <span class="s" style="color: #d14;">'green'</span><span class="p">},</span></span>
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198
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">row_extra_text</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="n" style="color: #333;">best_kmer_row</span><span class="p">:</span> <span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_left_arrow</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'best'</span><span class="p">})</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Report on the results of the read depth filter (can help with identifying levels of</span></span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># contamination).</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Read depth filter: removed {} contigs totalling {} bp'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">removed_count</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">removed_length</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"></span>
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200
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Clean up.</span></span>
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201
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">spades_dir</span><span class="p">):</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;"><span class="idiff left right">\n</span></span><span class="s" style="color: #d14;">Deleting '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">spades_dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Deleting '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">spades_dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span><span class="p">)</span></span>
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203
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">spades_dir</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_errors</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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204
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">spades_tmp_dir</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">spades_tmp_dir</span><span class="p">):</span></span>
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205
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Deleting '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">spades_tmp_dir</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'/'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb#e7416bd43296684326192cb201ec8dcbd20ab982"><strong>unicycler/src/miniasm/hit.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,6 +8,7 @@</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma GCC diagnostic ignored "-Wpragmas"</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma GCC diagnostic ignored "-Wunknown-warning-option"</span></span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma GCC diagnostic ignored "-Wvla"</span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma GCC diagnostic ignored "-Wvla-extension"</span></span>
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13
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"</span></span>
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<a href="https://salsa.debian.org/med-team/unicycler/commit/2c389812ce653b939b6147ece219cbcc695672fb#59fca07fac6fd9e5a326c480accace22111a2286"><strong>unicycler/unicycler.py</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">@@ -85,7 +85,7 @@ def main():</td>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">spades_path</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threads</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keep</span><span class="p">,</span></span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_count</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_kmer_frac</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_kmer_frac</span><span class="p">,</span></span>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmers</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">no_correct</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">linear_seqs</span><span class="p">,</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">spades_tmp_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">spades_tmp_dir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">largest_component</span></span><span class="p">)</span></span>
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89
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">determine_copy_depth</span><span class="p">(</span><span class="n" style="color: #333;">graph</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keep</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">best_spades_graph</span><span class="p">):</span></span>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">graph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">save_to_gfa</span><span class="p">(</span><span class="n" style="color: #333;">best_spades_graph</span><span class="p">,</span> <span class="n" style="color: #333;">save_copy_depth_info</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">newline</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -346,6 +346,10 @@ def get_arguments():</td>
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346
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Filter out contigs lower than this fraction of the chromosomal '</span></span>
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347
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"> <span class="s" style="color: #d14;">'depth, if doing so does not result in graph dead ends'</span></span>
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348
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">show_all_args</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">)</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">spades_group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--largest_component'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Only keep the largest connected component of the assembly '</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="s" style="color: #d14;">'graph (default: keep all connected components)'</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">show_all_args</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">)</span></span>
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349
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353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">spades_group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--spades_tmp_dir'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Specify SPAdes temporary directory using the SPAdes --tmp-dir "</span></span>
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="s" style="color: #d14;">"option (default: make a temporary directory in the output "</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -912,10 +916,10 @@ def rotate_completed_replicons(graph, args, counter):</td>
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912
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916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_section_header</span><span class="p">(</span><span class="s" style="color: #d14;">'Rotating completed replicons'</span><span class="p">)</span></span>
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917
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_explanation</span><span class="p">(</span><span class="s" style="color: #d14;">'Any completed circular contigs (i.e. single contigs which have one '</span></span>
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="python"> <span class="s" style="color: #d14;">'link connecting end to start) can have their start position changed '</span></span>
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="python"> <span class="s" style="color: #d14;">'with<span class="idiff left right"> altering the sequence. For consistency, Unicycler now searches</span> '</span></span>
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">for a starting gene (dnaA or repA) in each such contig, and if one</span> '</span></span>
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="python"> <span class="s" style="color: #d14;">'i<span class="idiff left right">s found, the contig is rotated to start with that gene on the</span> '</span></span>
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="python"> <span class="s" style="color: #d14;">'forward strand.'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="python"> <span class="s" style="color: #d14;">'with<span class="idiff left right">out altering the sequence. For consistency, Unicycler now</span> '</span></span>
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">searches for a starting gene (dnaA or repA) in each such contig, and</span> '</span></span>
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="python"> <span class="s" style="color: #d14;">'i<span class="idiff left right">f one is found, the contig is rotated to start with that gene on</span> '</span></span>
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="python"> <span class="s" style="color: #d14;">'<span class="idiff left right">the </span>forward strand.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="python"> <span class="n" style="color: #333;">rotation_result_table</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[</span><span class="s" style="color: #d14;">'Segment'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Length'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Depth'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Starting gene'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Position'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="python"> <span class="s" style="color: #d14;">'Strand'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Identity'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Coverage'</span><span class="p">]]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,4 +13,4 @@ details. You should have received a copy of the GNU General Public License along</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.4.<span class="idiff left right">7</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.4.<span class="idiff left right">8</span>'</span></span></pre>
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