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ChangeLog.txt
View file @ 3bfe2036
2019-08-21 Martin C. Frith <Martin C. Frith>
* doc/last-dotplot.txt, scripts/last-dotplot:
dotplot: change satellite-repeat color to purple
[fb43f850eba2] [tip]
2019-07-16 Martin C. Frith <Martin C. Frith>
* doc/last-split.txt, doc/last-tutorial.txt, scripts/last-train,
src/split/last-split-main.cc, test/last-split-test.out, test/last-
split-test.sh:
Change last-split -m default to 1
[2a722dbe737a] [tip]
[2a722dbe737a]
2019-06-27 Martin C. Frith <Martin C. Frith>
......
debian/changelog
View file @ 3bfe2036
last-align (984-1) unstable; urgency=medium
* Team upload.
* New upstream version
* Set fields Upstream-Contact in debian/copyright.
* Remove obsolete fields Name, Contact from debian/upstream/metadata.
-- Steffen Moeller <moeller@debian.org> Wed, 04 Sep 2019 14:05:53 +0200
last-align (983-1) unstable; urgency=medium
* Team upload.
......
debian/copyright
View file @ 3bfe2036
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: LAST
Source: http://last.cbrc.jp/
Upstream-Contact: last@cbrc.jp
Files: *
Copyright: © 2008–2015 Martin C. Frith
......@@ -26,4 +27,3 @@ License: GPL-3+
.
On Debian systems, the complete text of the GNU General Public
License can be found in `/usr/share/common-licenses/GPL-3'.
debian/upstream/metadata
View file @ 3bfe2036
Contact: last@cbrc.jp
Name: LAST
Reference:
- Author: Frith, Martin C. and Wan, Raymond and Horton, Paul
Title: >
Incorporating sequence quality data into alignment improves DNA read mapping
Title: "Incorporating sequence quality data into alignment improves DNA read mapping\n"
Journal: Nucl. Acids Res.
Volume: 38
Number: 7
......
doc/last-dotplot.html
View file @ 3bfe2036
......@@ -498,8 +498,8 @@ strand is &quot;+&quot;, pale blue if &quot;-&quot;, or pale purple.</td></tr>
<kbd><span class="option">--rmsk1=<var>FILE</var></span></kbd></td>
<td>Read repeat annotations for the 1st genome, in RepeatMasker .out
or rmsk.txt format. The color is pale purple for &quot;low
complexity&quot; and &quot;simple repeats&quot;, else pale red for &quot;+&quot; strand
and pale blue for &quot;-&quot; strand.</td></tr>
complexity&quot;, &quot;simple repeats&quot;, and &quot;satellites&quot;, else pale red
for &quot;+&quot; strand and pale blue for &quot;-&quot; strand.</td></tr>
<tr><td class="option-group">
<kbd><span class="option">--rmsk2=<var>FILE</var></span></kbd></td>
<td>Read repeat annotations for the 2nd genome.</td></tr>
......
doc/last-dotplot.txt
View file @ 3bfe2036
......@@ -137,8 +137,8 @@ gene annotations in one small dotplot.
--rmsk1=FILE
Read repeat annotations for the 1st genome, in RepeatMasker .out
or rmsk.txt format. The color is pale purple for "low
complexity" and "simple repeats", else pale red for "+" strand
and pale blue for "-" strand.
complexity", "simple repeats", and "satellites", else pale red
for "+" strand and pale blue for "-" strand.
--rmsk2=FILE
Read repeat annotations for the 2nd genome.
......
scripts/last-dotplot
View file @ 3bfe2036
......@@ -647,10 +647,10 @@ def readRmsk(fileName, rangeDict):
beg = int(fields[5]) - 1
end = int(fields[6])
strand = fields[8]
repeatClass = fields[10]
repeatClass = fields[10].split("/")[0]
else:
continue
if repeatClass in ("Low_complexity", "Simple_repeat"):
if repeatClass in ("Low_complexity", "Simple_repeat", "Satellite"):
yield 200, "#fbf", seqName, beg, end
elif (strand == "+") != rangeDict[seqName][0][2]:
yield 100, "#ffe8e8", seqName, beg, end
......