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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/last-align/commit/29a2a247153429a93415d57431a6bf7463fbfdab">29a2a247</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2019-09-04T12:05:43Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 984</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#57bf262130f956caf76c405086f0815caf4e0a89">
ChangeLog.txt
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<li class="file-stats">
<a href="#d569d86e42565e3be7e6f2dd351c600fe0f19a6f">
doc/last-dotplot.html
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<li class="file-stats">
<a href="#1b4eb23521879045d9184d50996b3aa277a711e9">
doc/last-dotplot.txt
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<a href="#d6f8248b8a5e868eac831cf1a35c8543f1fff6a8">
scripts/last-dotplot
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<li class="file-stats">
<a href="#69737f84c540417aafef4e696f66adcc9f92fa66">
src/version.hh
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<h4>Changes:</h4>
<li id="57bf262130f956caf76c405086f0815caf4e0a89">
<a href="https://salsa.debian.org/med-team/last-align/commit/29a2a247153429a93415d57431a6bf7463fbfdab#57bf262130f956caf76c405086f0815caf4e0a89"><strong>ChangeLog.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2019-08-21 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * doc/last-dotplot.txt, scripts/last-dotplot:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> dotplot: change satellite-repeat color to purple</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [fb43f850eba2] [tip]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">2019-07-16 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * doc/last-split.txt, doc/last-tutorial.txt, scripts/last-train,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> src/split/last-split-main.cc, test/last-split-test.out, test/last-</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> split-test.sh:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> Change last-split -m default to 1</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> [2a722dbe737a]<span class="idiff left right"> [tip]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [2a722dbe737a]</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">2019-06-27 Martin C. Frith <Martin C. Frith></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/last-align/commit/29a2a247153429a93415d57431a6bf7463fbfdab#d569d86e42565e3be7e6f2dd351c600fe0f19a6f"><strong>doc/last-dotplot.html</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="498" style="width: 35px; color: rgba(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">@@ -498,8 +498,8 @@ strand is "+", pale blue if "-", or pale purple.</td></tr></td>
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498
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--rmsk1=<span class="nt" style="color: #000080;"><var></span>FILE<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Read repeat annotations for the 1st genome, in RepeatMasker .out</span>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="html">or rmsk.txt format. The color is pale purple for <span class="ni" style="color: #800080;">"</span>low</span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="html">complexity<span class="ni" style="color: #800080;">"</span><span class="idiff left"> and </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">simple repeats</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">, else pale red for </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">+</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right"> stran</span>d</span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="html">and pale blue for <span class="ni" style="color: #800080;">"</span>-<span class="ni" style="color: #800080;">"</span> strand.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="html">complexity<span class="ni" style="color: #800080;">"</span><span class="idiff left">, </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">simple repeats</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">, and </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">satellites</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right">, else pale re</span>d</span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="html"><span class="idiff left">for </span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff">+</span><span class="ni" style="color: #800080;"><span class="idiff">"</span></span><span class="idiff right"> strand </span>and pale blue for <span class="ni" style="color: #800080;">"</span>-<span class="ni" style="color: #800080;">"</span> strand.<span class="nt" style="color: #000080;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="html"><span class="nt" style="color: #000080;"><tr><td</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option-group"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="html"><span class="nt" style="color: #000080;"><kbd><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"option"</span><span class="nt" style="color: #000080;">></span>--rmsk2=<span class="nt" style="color: #000080;"><var></span>FILE<span class="nt" style="color: #000080;"></var></span></kbd></td></span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="html"><span class="nt" style="color: #000080;"><td></span>Read repeat annotations for the 2nd genome.<span class="nt" style="color: #000080;"></td></tr></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">@@ -137,8 +137,8 @@ gene annotations in one small dotplot.</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"> --rmsk1=FILE</span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"> Read repeat annotations for the 1st genome, in RepeatMasker .out</span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"> or rmsk.txt format. The color is pale purple for "low</span>
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"> complexity"<span class="idiff left right"> and "simple repeats", else pale red for "+" stran</span>d</span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"> and pale blue for "-" strand.</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> complexity"<span class="idiff left right">, "simple repeats", and "satellites", else pale re</span>d</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> <span class="idiff left right">for "+" strand </span>and pale blue for "-" strand.</span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"> --rmsk2=FILE</span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext"> Read repeat annotations for the 2nd genome.</span>
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<pre style="margin: 0;"> <span id="LC144" 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">@@ -647,10 +647,10 @@ def readRmsk(fileName, rangeDict):</td>
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<pre style="margin: 0;"> <span id="LC647" 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="LC648" 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="LC649" 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="LC650" 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>
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<pre style="margin: 0;">+<span id="LC650" 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="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"/"</span></span><span class="p"><span class="idiff">)[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span></span></span>
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<pre style="margin: 0;"> <span id="LC651" 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="LC652" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">-<span id="LC653" 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>
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<pre style="margin: 0;">+<span id="LC653" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"Satellite"</span></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;">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>
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<pre style="margin: 0;"> <span id="LC655" 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="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;">2</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC656" 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>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"98<span class="idiff left right">3</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="s" style="color: #d14;">"98<span class="idiff left right">4</span>"</span></span></pre>
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