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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/b3ca634d131e8470dfda044c9aadb1cfbe22c4f9">b3ca634d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-08-23T00:56:26+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1256</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#217c6bc12768d15897bf0441140820b8ec85a125">
bin/last-dotplot
</a>
</li>
<li class="file-stats">
<a href="#3005ac7967e4a8278470a34d68f44dcd2b1b63cd">
doc/last-dotplot.rst
</a>
</li>
<li class="file-stats">
<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
</a>
</li>
<li class="file-stats">
<a href="#b8658dba55bc28b741dfef5e4ea001b2623bdb9e">
src/mcf_frameshift_xdrop_aligner.cc
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="217c6bc12768d15897bf0441140820b8ec85a125">
<a href="https://salsa.debian.org/med-team/last-align/-/commit/b3ca634d131e8470dfda044c9aadb1cfbe22c4f9#217c6bc12768d15897bf0441140820b8ec85a125"><strong>bin/last-dotplot</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -589,112 +589,121 @@ def expandedSeqDict(seqDict):</td>
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589
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589
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="python"> <span class="n" style="color: #333;">newDict</span><span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span></span>
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590
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590
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">newDict</span></span>
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591
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591
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python"></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readBed</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">):</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span></span>
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594
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="python"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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595
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">w</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">isdigit</span><span class="p">():</span></span>
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597
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="python"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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598
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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600
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<pre style="margin: 0;">-<span id="LC600" class="line" lang="python"> <span class="n" style="color: #333;">seqRanges</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">[</span><span class="n" style="color: #333;">seqName</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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602
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</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="LC603" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqRanges</span><span class="p">):</span></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC605" class="line" lang="python"> <span class="n" style="color: #333;">itemName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"."</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">commaSeparatedInts</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">))</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="python"></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">annotsFromBedOrAgp</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">):</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">7</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">].</span><span class="n" style="color: #333;">isalpha</span><span class="p">():</span> <span class="c1" style="color: #998; font-style: italic;"># agp format, or gap.txt</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"NU"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">].</span><span class="n" style="color: #333;">isdigit</span><span class="p">():</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># zero-based coordinate</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"yes"</span><span class="p">:</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">30000</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">bridged_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">20000</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">unbridged_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># BED format</span></span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">itemName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"."</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span></span>
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606
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">layer</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">900</span></span>
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607
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"#fbf"</span></span>
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">w</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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609
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left right">w</span></span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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="LC610" class="line" lang="python"> <span class="n" style="color: #333;">layer</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">w</span></span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>
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611
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<pre style="margin: 0;">-<span id="LC611" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">w</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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612
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<pre style="margin: 0;">-<span id="LC612" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">w</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;"><span class="idiff right">w</span></span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</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="LC613" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"rgb("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">w</span></span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span></span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">fields</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left right">fields</span></span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</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="LC613" class="line" lang="python"> <span class="n" style="color: #333;">layer</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">fields</span></span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">fields</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fields</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;"><span class="idiff right">fields</span></span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</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="LC616" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"rgb("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;"><span class="idiff left right">fields</span></span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">")"</span></span>
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">w</span></span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="python"> <span class="n" style="color: #333;">isRev</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">seqRanges</span></span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">fields</span></span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"> <span class="n" style="color: #333;">isRev</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">rangeDict</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">seqName</span></span><span class="p"><span class="idiff right">]</span>[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</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;">isRev</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isRev</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"#ffe8e8"</span></span>
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</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;">isRev</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isRev</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"#e8e8ff"</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">layer</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">itemName</span></span>
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC623" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">commaSeparatedInts</span><span class="p">(</span><span class="n" style="color: #333;">text</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC626" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readGenePred</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># xxx tab ???</span></span>
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<pre style="margin: 0;">-<span id="LC629" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">fields</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="python"> <span class="n" style="color: #333;">geneName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">12</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">12</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># XXX ???</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">seqRanges</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">[</span><span class="n" style="color: #333;">seqName</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC636" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#strand = fields[2]</span></span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">annotsFromGpd</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">fields</span><span class="p">,</span> <span class="n" style="color: #333;">geneName</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># xxx split on tabs?</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"> <span class="n" style="color: #333;">cdsBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"> <span class="n" style="color: #333;">cdsEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"> <span class="n" style="color: #333;">exonBegs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">commaSeparatedInts</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"> <span class="n" style="color: #333;">exonEnds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">commaSeparatedInts</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">exonBegs</span><span class="p">,</span> <span class="n" style="color: #333;">exonEnds</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqRanges</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">exon_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">geneName</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">cdsBeg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">cdsEnd</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">e</span><span class="p">:</span> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">400</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">cds_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC649" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readRmsk</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">17</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># rmsk.txt</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># do this ASAP for speed</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="python"> <span class="n" style="color: #333;">repeatName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</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="LC659" class="line" lang="python"> <span class="n" style="color: #333;">repeatClass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">15</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># .out</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</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="LC664" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC665" class="line" lang="python"> <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python"> <span class="n" style="color: #333;">repeatName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="python"> <span class="n" style="color: #333;">repeatClass</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC668" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC669" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="python"> <span class="n" style="color: #333;">seqRanges</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">[</span><span class="n" style="color: #333;">seqName</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqRanges</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">repeatClass</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"Low_complexity"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Simple_repeat"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Satellite"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">200</span><span class="p">,</span> <span class="s" style="color: #d14;">"#fbf"</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">repeatName</span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">seqRanges</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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676
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="s" style="color: #d14;">"#ffe8e8"</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">repeatName</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="s" style="color: #d14;">"#e8e8ff"</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">repeatName</span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isExtraFirstGapField</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC681" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">].</span><span class="n" style="color: #333;">isdigit</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readGaps</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="python"> <span class="s" style="color: #d14;">'''Read locations of unsequenced gaps, from an agp or gap file.'''</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="python"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">w</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"#"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isExtraFirstGapField</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">):</span> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"NU"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</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="LC693" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="c1" style="color: #998; font-style: italic;"># zero-based coordinate</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"yes"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">3000</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">bridged_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">2000</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">unbridged_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">annotsFromGff</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">):</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="python"> <span class="n" style="color: #333;">feature</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</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="LC642" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</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="LC643" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">feature</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"exon"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"> <span class="n" style="color: #333;">geneName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">";"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">geneName</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"="</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">geneName</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">geneName</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">).</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">";"</span><span class="p">)</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">re</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'[= ]'</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"gene"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrs</span><span class="p">:</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="python"> <span class="n" style="color: #333;">geneName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">"gene"</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># seems good for NCBI gff</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">"Name"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">attrs</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">geneName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">"Name"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="python"> <span class="n" style="color: #333;">geneName</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">300</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">exon_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">geneName</span></span>
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656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">feature</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"CDS"</span><span class="p">:</span></span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">400</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">cds_color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python"></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">annotsFromRep</span><span class="p">(</span><span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">repName</span><span class="p">,</span> <span class="n" style="color: #333;">repClass</span><span class="p">):</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"> <span class="n" style="color: #333;">simple</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Low_complexity"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Simple_repeat"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Satellite"</span></span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">repClass</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="n" style="color: #333;">simple</span><span class="p">):</span></span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">200</span><span class="p">,</span> <span class="s" style="color: #d14;">"#fbf"</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">repName</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"+"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="n" style="color: #333;">rangeDict</span><span class="p">[</span><span class="n" style="color: #333;">seqName</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="s" style="color: #d14;">"#ffe8e8"</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">repName</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="s" style="color: #d14;">"#e8e8ff"</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">repName</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">annotsFromFiles</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">fileNames</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">):</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="python"> <span class="n" style="color: #333;">isDig</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;">isdigit</span></span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fileName</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fileNames</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">myOpen</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">)</span></span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"+C-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]):</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># RepeatMasker .out</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span> <span class="c1" style="color: #998; font-style: italic;"># do this ASAP for speed</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotsFromRep</span><span class="p">(</span><span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">])</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">11</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"+-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]):</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># rmsk.txt</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">])</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">])</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotsFromRep</span><span class="p">(</span><span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">],</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">])</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">8</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"+-."</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]):</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python"> <span class="n" style="color: #333;">seqName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqName</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotsFromGff</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">)</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">9</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"+-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]):</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python"> <span class="n" style="color: #333;">geneName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">12</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">12</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># XXX ???</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotsFromGpd</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">,</span> <span class="n" style="color: #333;">geneName</span><span class="p">)</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">10</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"+-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]):</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python"> <span class="n" style="color: #333;">geneName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">12</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">12</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># XXX ???</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotsFromGpd</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:],</span> <span class="n" style="color: #333;">geneName</span><span class="p">)</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]):</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotsFromBedOrAgp</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">)</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">n</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;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">isDig</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]):</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annotsFromBedOrAgp</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"#"</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">g</span><span class="p">:</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="python"> <span class="n" style="color: #333;">layer</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="n" style="color: #333;">seqName</span><span class="p">,</span> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">r</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">[</span><span class="n" style="color: #333;">seqName</span><span class="p">]):</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">i</span></span>
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="python"></span>
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">bedBoxes</span><span class="p">(</span><span class="n" style="color: #333;">annots</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">,</span> <span class="n" style="color: #333;">limit</span><span class="p">,</span> <span class="n" style="color: #333;">isTop</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix</span><span class="p">):</span></span>
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700
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"> <span class="n" style="color: #333;">beds</span><span class="p">,</span> <span class="n" style="color: #333;">textSizes</span><span class="p">,</span> <span class="n" style="color: #333;">margin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annots</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); 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="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -707,7 +716,7 @@ def bedBoxes(annots, rangeDict, limit, isTop, bpPerPix):</td>
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707
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">beg</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">end</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>
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708
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">isReverseRange</span><span class="p">:</span></span>
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">beg</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">beg</span></span>
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710
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">layer</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1000</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">layer</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1000<span class="idiff left right">0</span></span><span class="p">:</span></span>
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711
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># include partly-covered pixels</span></span>
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712
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721
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python"> <span class="n" style="color: #333;">pixBeg</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">origin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">beg</span><span class="p">)</span> <span class="o" style="font-weight: 600;">//</span> <span class="n" style="color: #333;">bpPerPix</span></span>
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713
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"> <span class="n" style="color: #333;">pixEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">div_ceil</span><span class="p">(</span><span class="n" style="color: #333;">origin</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">bpPerPix</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">@@ -855,13 +864,9 @@ def remainingSequenceRanges(seqRanges, alignments, seqIndex):</td>
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855
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">remainingSequences</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="n" style="color: #333;">seqIndex</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignments</span><span class="p">)</span></span>
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856
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seqRanges</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">remainingSequences</span><span class="p">]</span></span>
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857
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readAnnotations</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">textDraw</span><span class="p">,</span> <span class="n" style="color: #333;">sortedRanges</span><span class="p">,</span> <span class="n" style="color: #333;">totalLength</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC859" class="line" lang="python"> <span class="n" style="color: #333;">bedFile</span><span class="p">,</span> <span class="n" style="color: #333;">repFile</span><span class="p">,</span> <span class="n" style="color: #333;">geneFile</span><span class="p">,</span> <span class="n" style="color: #333;">gapFile</span><span class="p">):</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readAnnots</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">textDraw</span><span class="p">,</span> <span class="n" style="color: #333;">sortedRanges</span><span class="p">,</span> <span class="n" style="color: #333;">totalLength</span><span class="p">,</span> <span class="n" style="color: #333;">fileNames</span><span class="p">):</span></span>
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python"> <span class="n" style="color: #333;">rangeDict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">expandedSeqDict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">rangesPerSeq</span><span class="p">(</span><span class="n" style="color: #333;">sortedRanges</span><span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">annots</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">chain</span><span class="p">(</span><span class="n" style="color: #333;">readBed</span><span class="p">(</span><span class="n" style="color: #333;">bedFile</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">),</span></span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">readRmsk</span><span class="p">(</span><span class="n" style="color: #333;">repFile</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">),</span></span>
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863
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">readGenePred</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">geneFile</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">),</span></span>
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864
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">readGaps</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">gapFile</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">)))</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="python"> <span class="n" style="color: #333;">annots</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">annotsFromFiles</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">fileNames</span><span class="p">,</span> <span class="n" style="color: #333;">rangeDict</span><span class="p">))</span></span>
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865
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">annots</span><span class="p">)</span></span>
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="python"> <span class="n" style="color: #333;">textSizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">sizesPerText</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">textDraw</span><span class="p">))</span></span>
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="python"> <span class="n" style="color: #333;">maxTextLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">totalLength</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -937,12 +942,12 @@ def lastDotplot(opts, args):</td>
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937
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942
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="python"></span>
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"reading annotations..."</span><span class="p">)</span></span>
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944
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC940" class="line" lang="python"> <span class="n" style="color: #333;">annots1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readAnnot<span class="idiff left right">ation</span>s</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">textDraw</span><span class="p">,</span> <span class="n" style="color: #333;">sortedRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">height</span><span class="p">,</span></span>
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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">bed1</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rmsk1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">genePred1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">gap1</span></span><span class="p">)</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="python"> <span class="n" style="color: #333;">annots1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readAnnots</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">textDraw</span><span class="p">,</span> <span class="n" style="color: #333;">sortedRanges1</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">height</span><span class="p">,</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="python"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">bed1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="python"> <span class="n" style="color: #333;">bMargin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annots1</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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948
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="python"> <span class="n" style="color: #333;">annots2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readAnnot<span class="idiff left right">ation</span>s</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">textDraw</span><span class="p">,</span> <span class="n" style="color: #333;">sortedRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">width</span><span class="p">,</span></span>
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945
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">bed2</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rmsk2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">genePred2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opts</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">gap2</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="python"> <span class="n" style="color: #333;">annots2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readAnnots</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">font</span><span class="p">,</span> <span class="n" style="color: #333;">textDraw</span><span class="p">,</span> <span class="n" style="color: #333;">sortedRanges2</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">width</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="python"> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">bed2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC951" class="line" lang="python"> <span class="n" style="color: #333;">rMargin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">annots2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC952" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="python"> <span class="n" style="color: #333;">maxPixels1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lMargin</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">rMargin</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1057,10 +1062,6 @@ if __name__ == "__main__":</td>
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--seq2"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PATTERN"</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;">"append"</span><span class="p">,</span></span>
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>
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1059
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1064
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<pre style="margin: 0;"> <span id="LC1064" 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;">"which sequences to show from the 2nd genome"</span><span class="p">)</span></span>
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1060
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<pre style="margin: 0;">-<span id="LC1060" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--forwardcolor"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"red"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1061" 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;">"color for forward alignments (default: %default)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1062" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--reversecolor"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"blue"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1063" 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;">"color for reverse alignments (default: %default)"</span><span class="p">)</span></span>
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1064
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--alignments"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"secondary alignments"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--sort1"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"N"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1067" 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;">"genome1 sequence order: 0=input order, 1=name order, "</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">@@ -1088,11 +1089,12 @@ if __name__ == "__main__":</td>
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1088
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1089
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<pre style="margin: 0;"> <span id="LC1089" class="line" lang="python"> <span class="s" style="color: #d14;">"2=alignments adjacent in genome2 (default=%default)"</span><span class="p">)</span></span>
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1090
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<pre style="margin: 0;"> <span id="LC1090" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--border-pixels"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"INT"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"int"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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1090
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1091
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<pre style="margin: 0;"> <span id="LC1091" 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;">"number of pixels between sequences (default=%default)"</span><span class="p">)</span></span>
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1091
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<pre style="margin: 0;">-<span id="LC1091" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--border-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"black"</span><span class="p">,</span></span>
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1092
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<pre style="margin: 0;">-<span id="LC1092" 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;">"color for pixels between sequences (default=%default)"</span><span class="p">)</span></span>
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1093
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<pre style="margin: 0;">-<span id="LC1093" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># --break-color and/or --break-pixels for intra-sequence breaks?</span></span>
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1094
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--margin-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#dcdcdc"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1095" 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;">"margin color"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--bed1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--rmsk1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--genePred1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--gap1"</span><span class="p">,</span></span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"append"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1094" 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;">"read genome1 annotations"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--bed2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--rmsk2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--genePred2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--gap2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"append"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1097" 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;">"read genome2 annotations"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Text options"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--fontfile"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</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">@@ -1111,33 +1113,20 @@ if __name__ == "__main__":</td>
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1113
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<pre style="margin: 0;"> <span id="LC1113" 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;">"text rotation for the 2nd genome (default=%default)"</span><span class="p">)</span></span>
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1112
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1114
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<pre style="margin: 0;"> <span id="LC1114" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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1113
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1115
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="python"></span>
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1114
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<pre style="margin: 0;">-<span id="LC1114" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Annotation options"</span><span class="p">)</span></span>
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1115
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<pre style="margin: 0;">-<span id="LC1115" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--bed1"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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1116
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<td class="new_line diff-line-num old" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1116" 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;">"read genome1 annotations from BED file"</span><span class="p">)</span></span>
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1117
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<pre style="margin: 0;">-<span id="LC1117" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--bed2"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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1118
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<pre style="margin: 0;">-<span id="LC1118" 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;">"read genome2 annotations from BED file"</span><span class="p">)</span></span>
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1119
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<pre style="margin: 0;">-<span id="LC1119" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--rmsk1"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"read genome1 repeats from "</span></span>
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<pre style="margin: 0;">-<span id="LC1120" class="line" lang="python"> <span class="s" style="color: #d14;">"RepeatMasker .out or rmsk.txt file"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1121" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--rmsk2"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"read genome2 repeats from "</span></span>
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<pre style="margin: 0;">-<span id="LC1122" class="line" lang="python"> <span class="s" style="color: #d14;">"RepeatMasker .out or rmsk.txt file"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1123" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1124" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC1125" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Gene options"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1126" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--genePred1"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1127" 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;">"read genome1 genes from genePred file"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1128" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--genePred2"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1129" 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;">"read genome2 genes from genePred file"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Color options"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--forwardcolor"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"red"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" 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;">"color for forward alignments (default: %default)"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--reversecolor"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"blue"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1120
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<pre style="margin: 0;">+<span id="LC1120" 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;">"color for reverse alignments (default: %default)"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--border-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"black"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1122
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<pre style="margin: 0;">+<span id="LC1122" 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;">"color for pixels between sequences (default=%default)"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># --break-color and/or --break-pixels for intra-sequence breaks?</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--margin-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"#dcdcdc"</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1125
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<pre style="margin: 0;">+<span id="LC1125" 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;">"margin color"</span><span class="p">)</span></span>
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1130
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<td class="new_line diff-line-num" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--exon-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PaleGreen"</span><span class="p">,</span></span>
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1131
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<td class="new_line diff-line-num" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1127
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<pre style="margin: 0;"> <span id="LC1127" 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;">"color for exons (default=%default)"</span><span class="p">)</span></span>
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1132
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<td class="new_line diff-line-num" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--cds-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"LimeGreen"</span><span class="p">,</span></span>
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1133
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<td class="new_line diff-line-num" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1129
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<pre style="margin: 0;"> <span id="LC1129" 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;">"color for protein-coding regions (default=%default)"</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1134
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<td class="new_line diff-line-num old" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1134" class="line" lang="python"> <span class="n" style="color: #333;">op</span><span class="p">.</span><span class="n" style="color: #333;">add_option_group</span><span class="p">(</span><span class="n" style="color: #333;">og</span><span class="p">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1135
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<td class="new_line diff-line-num old" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1135" class="line" lang="python"></span>
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<td class="old_line diff-line-num old" data-linenumber="1136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1136
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<td class="new_line diff-line-num old" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1136" class="line" lang="python"> <span class="n" style="color: #333;">og</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optparse</span><span class="p">.</span><span class="n" style="color: #333;">OptionGroup</span><span class="p">(</span><span class="n" style="color: #333;">op</span><span class="p">,</span> <span class="s" style="color: #d14;">"Unsequenced gap options"</span><span class="p">)</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1137
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<td class="new_line diff-line-num old" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1137" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--gap1"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1138
</td>
<td class="new_line diff-line-num old" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1138" 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;">"read genome1 unsequenced gaps from agp or gap file"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1139" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--gap2"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"FILE"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1140" 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;">"read genome2 unsequenced gaps from agp or gap file"</span><span class="p">)</span></span>
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1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--bridged-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"yellow"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC1131" 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;">"color for bridged gaps (default: %default)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="python"> <span class="n" style="color: #333;">og</span><span class="p">.</span><span class="n" style="color: #333;">add_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--unbridged-color"</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COLOR"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"orange"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/b3ca634d131e8470dfda044c9aadb1cfbe22c4f9#3005ac7967e4a8278470a34d68f44dcd2b1b63cd"><strong>doc/last-dotplot.rst</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">@@ -2,7 +2,7 @@ last-dotplot</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">============</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">This script makes a dotplot, a.k.a. Oxford Grid, of pair-wise sequence</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">alignments in MAF or LAST tabular format. It requires the `Python</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">alignments in MAF<span class="idiff left right">_</span> or LAST tabular format. It requires the `Python</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Imaging Library`_ to be installed. It can be used like this::</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> last-dotplot my-alignments my-plot.png</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">@@ -11,6 +11,10 @@ The output can be in any format supported by the Imaging Library::</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> last-dotplot alns alns.gif</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">It can read alignments from a pipe like this::</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ... | last-dotplot - my-plot.png</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Terminology</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">-----------</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></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">@@ -37,10 +41,14 @@ Options</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> Which sequences to show from the 1st (horizontal) genome.</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext">-2 PATTERN, --seq2=PATTERN</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> Which sequences to show from the 2nd (vertical) genome.</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">-c COLOR, --forwardcolor=COLOR</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> Color for forward alignments.</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">-r COLOR, --reversecolor=COLOR</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> Color for reverse alignments.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">-a FILE</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> Read annotations for the 1st (horizontal) genome, and draw them as</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> vertical stripes. For backwards compatibility, these options have</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> the same meaning: ``--bed1 --rmsk1 --genePred1 --gap1``.</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">-b FILE</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> Read annotations for the 2nd (vertical) genome, and draw them as</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> horizontal stripes. For backwards compatibility, these options</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> have the same meaning: ``--bed2 --rmsk2 --genePred2 --gap2``.</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">--alignments=FILE</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> Read secondary alignments. For example: we could use primary</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"> alignment data with one human DNA read aligned to the human</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">@@ -91,10 +99,6 @@ Options</td>
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91
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> in the 2nd (vertical) genome.</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">--border-pixels=INT</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> Number of pixels between sequences.</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">--border-color=COLOR</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"> Color for pixels between sequences.</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">--margin-color=COLOR</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext"> Color for the margins.</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext">Text options</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">~~~~~~~~~~~~</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">@@ -116,58 +120,49 @@ Text options</td>
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116
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">--rot2=ROT</span>
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117
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext"> Text rotation for the 2nd genome: h(orizontal) or v(ertical).</span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">Annotation options</span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~</span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">These options read annotations of sequence segments, and draw them as</span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">colored horizontal or vertical stripes. This looks good only if the</span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">annotations are reasonably sparse: e.g. you can't sensibly view 20000</span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">gene annotations in one small dotplot.</span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext">--bed1=FILE</span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext"> Read BED-format_ annotations for the 1st genome. They are drawn</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"> as stripes, with coordinates given by the first three BED fields.</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext"> The color is specified by the RGB field if present, else pale red</span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext"> if the strand is "+", pale blue if "-", or pale purple.</span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">--bed2=FILE</span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> Read BED-format annotations for the 2nd genome.</span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">--rmsk1=FILE</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> Read repeat annotations for the 1st genome, in RepeatMasker .out</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"> or rmsk.txt format. The color is pale purple for "low</span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"> complexity", "simple repeats", and "satellites", else pale red</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext"> for "+" strand and pale blue for "-" strand.</span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext">--rmsk2=FILE</span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> Read repeat annotations for the 2nd genome.</span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">Gene options</span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext">~~~~~~~~~~~~</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">Color options</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">~~~~~~~~~~~~~</span>
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144
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">--genePred1=FILE</span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"> Read gene annotations for the 1st genome in `genePred format`_.</span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext">--genePred2=FILE</span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext"> Read gene annotations for the 2nd genome.</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">-c COLOR, --forwardcolor=COLOR</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> Color for forward alignments.</span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">-r COLOR, --reversecolor=COLOR</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> Color for reverse alignments.</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">--border-color=COLOR</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> Color for pixels between sequences.</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">--margin-color=COLOR</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> Color for the margins.</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
149
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134
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC134" class="line" lang="plaintext">--exon-color=COLOR</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
150
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135
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC135" class="line" lang="plaintext"> Color for exons.</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
151
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<td class="new_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC136" class="line" lang="plaintext">--cds-color=COLOR</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
152
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"> Color for protein-coding regions.</span>
</pre>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">--bridged-color=COLOR</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> Color for unsequenced gaps with "yes" evidence of linkage.</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">--unbridged-color=COLOR</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> Color for unsequenced gaps with "no" evidence of linkage.</span>
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153
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext"><span class="idiff left right">Unsequenced gap op</span>tions</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"><span class="idiff left right">~~~~~~~~~~~~~~~~~~~~~~~</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"><span class="idiff left right">Annota</span>tions</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"><span class="idiff left right">-----------</span></span>
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156
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="plaintext"></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext">Note: these "gaps" are *not* alignment gaps (indels): they are regions</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext">of unknown sequence.</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">Options ``-a`` and ``-b`` can read annotations in these formats:</span>
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159
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext"></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext">--gap1=FILE</span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"> Read unsequenced gaps in the 1st genome from an agp or gap file.</span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext">--gap2=FILE</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"> Read unsequenced gaps in the 2nd genome from an agp or gap file.</span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext">--bridged-color=COLOR</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"> Color for bridged gaps.</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext">--unbridged-color=COLOR</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"> Color for unbridged gaps.</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">* BED_: The color is specified by the RGB field if present, else pale</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> red if the strand is "+", pale blue if "-", or pale purple. BED</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> lines with higher score are drawn on top of ones with lower score.</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">* Repeatmasker_ .out, rmsk.txt: The color is pale purple for "low</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> complexity", "simple repeats", and "satellites", else pale red for</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> "+" strand and pale blue for "-" strand.</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">* genePred_, GFF/GTF: Exons are shown in green, with a darker shade</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> for protein-coding regions.</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">* AGP_, gap.txt: Unsequenced gaps are shown, but only if the gap</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> covers at least one whole pixel.</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext">An unsequenced gap will be shown only if it covers at least one whole</span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext">pixel.</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">You can use these options multiple times, e.g. ``-a stuff.bed -a</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">more.bed -a rmsk.txt``. Annotations look good only if reasonably</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">sparse, e.g. you can't sensibly view 20000 gene annotations in one</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">small dotplot.</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">Choosing sequences</span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">------------------</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">@@ -224,5 +219,8 @@ Colors can be specified in `various ways described here</td>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext"><https://pillow.readthedocs.io/en/stable/reference/ImageColor.html>`_.</span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext">.. _Python Imaging Library: https://pillow.readthedocs.io/</span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="plaintext">.. _BED-format: https://genome.ucsc.edu/FAQ/FAQformat.html#format1</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="plaintext">.. _genePred format: https://genome.ucsc.edu/FAQ/FAQformat.html#format9</span></pre>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">.. _MAF: https://genome.ucsc.edu/FAQ/FAQformat.html#format5</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">.. _BED: https://genome.ucsc.edu/FAQ/FAQformat.html#format1</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">.. _genePred: https://genome.ucsc.edu/FAQ/FAQformat.html#format9</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">.. _RepeatMasker: http://www.repeatmasker.org/</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">.. _AGP: https://www.ncbi.nlm.nih.gov/assembly/agp/</span></pre>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/b3ca634d131e8470dfda044c9aadb1cfbe22c4f9#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</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">@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="make"> ../build/mat-inc.sh ../data/<span class="k" style="font-weight: 600;">*</span>.mat <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION1</span> <span class="o" style="font-weight: 600;">=</span> git describe <span class="nt" style="color: #000080;">--dirty</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 125<span class="idiff left right">4</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 125<span class="idiff left right">6</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\"</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-e</span> ../.git <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(VERSION1)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$(VERSION2)</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/commit/b3ca634d131e8470dfda044c9aadb1cfbe22c4f9#b8658dba55bc28b741dfef5e4ea001b2623bdb9e"><strong>src/mcf_frameshift_xdrop_aligner.cc</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">@@ -19,46 +19,59 @@ double FrameshiftXdropAligner::forward(const uchar *protein,</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">const_dbl_ptr</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">GapCosts</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gapCosts</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">probDropLimit</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isRightwardExtension</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isRightwardExtension</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">protein</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">frame0</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">frame1</span><span class="p">;</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">frame2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">proteinPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protein</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">frames</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">frames</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame0</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">seqIncrement</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">frames</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">frames</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">frame2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqIncrement</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isRightwardExtension</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">runOfDrops</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="LC41" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">runOfEdges</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="LC42" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numCells</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// number of DynProg cells in this antidiagonal</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">proteinEnd</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos6</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// xxx or 0 ?</span></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">diagPos6</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diagPos6</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos5</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos4</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">horiPos3</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">padSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// xxx or + padSize ?</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</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="LC39" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">thisPos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numCells</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xdropShape</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">xdropShape</span><span class="p">.</span><span class="n" style="color: #333;">resize</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="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">xdropShape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vertPos2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">xdropShape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinEnd</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">xdropShape</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">thisPos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">xFwdProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">yFwdProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">zFwdProbs</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">xFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">yFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">zFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">vertPos1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">sumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">logSumOfProbRatios</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="LC57" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xdropShape</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="n" style="color: #333;">xdropShape</span><span class="p">.</span><span class="n" style="color: #333;">assign</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">thisPos</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">frames</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// at end of DNA sequence</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">numOfAntidiagonals</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">rescaledSumOfProbRatios</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insOpenProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProbPieces</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">openProb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">delProb3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">delProb3</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb2</span><span class="p">;</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">insProb3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapCosts</span><span class="p">.</span><span class="n" style="color: #333;">insProb3</span><span class="p">;</span></span>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"></span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">resizeFwdProbsIfSmaller</span><span class="p">(</span><span class="n" style="color: #333;">thisPos</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">behindProb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">protein</span><span class="p">][</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">frame0</span><span class="p">];</span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">behindProb</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// XXX might fail?</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">xFwdProbs</span><span class="p">[</span><span class="n" style="color: #333;">padSize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">behindProb</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// xxx or padSize ?</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">runOfDrops</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="LC74" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">runOfEdges</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">substitutionProbs</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">protein</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seqIncrement</span><span class="p">)][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proteinPtr</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -147,7 +160,6 @@ double FrameshiftXdropAligner::forward(const uchar *protein,</td>
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147
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"> <span class="p">}</span></span>
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148
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"></span>
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149
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">rescaleStep</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">sumOfProbRatios</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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151
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sumOfProbRatios</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">numOfRescales</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">antidiagonal</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rescaleStep</span><span class="p">;</span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rescales</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numOfRescales</span><span class="p">)</span> <span class="n" style="color: #333;">rescales</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">numOfRescales</span><span class="p">);</span></span>
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