[med-svn] [Git][med-team/last-align][master] 6 commits: New upstream version 984
Steffen Möller
gitlab at salsa.debian.org
Wed Sep 4 13:09:43 BST 2019
Steffen Möller pushed to branch master at Debian Med / last-align
Commits:
29a2a247 by Steffen Moeller at 2019-09-04T12:05:43Z
New upstream version 984
- - - - -
577713bc by Steffen Moeller at 2019-09-04T12:05:43Z
New upstream version
- - - - -
ae0edab3 by Steffen Moeller at 2019-09-04T12:05:45Z
Update upstream source from tag 'upstream/984'
Update to upstream version '984'
with Debian dir f1215b2a9a5d8622858c8cedaf09f407836b5787
- - - - -
65791f1c by Steffen Moeller at 2019-09-04T12:05:52Z
Set fields Upstream-Contact in debian/copyright.
- - - - -
094338d9 by Steffen Moeller at 2019-09-04T12:05:52Z
Remove obsolete fields Name, Contact from debian/upstream/metadata.
- - - - -
3bfe2036 by Steffen Moeller at 2019-09-04T12:08:09Z
Upload to unstable
- - - - -
8 changed files:
- ChangeLog.txt
- debian/changelog
- debian/copyright
- debian/upstream/metadata
- doc/last-dotplot.html
- doc/last-dotplot.txt
- scripts/last-dotplot
- src/version.hh
Changes:
=====================================
ChangeLog.txt
=====================================
@@ -1,10 +1,16 @@
+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
=====================================
@@ -1,3 +1,12 @@
+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 at debian.org> Wed, 04 Sep 2019 14:05:53 +0200
+
last-align (983-1) unstable; urgency=medium
* Team upload.
=====================================
debian/copyright
=====================================
@@ -1,6 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: LAST
Source: http://last.cbrc.jp/
+Upstream-Contact: last at 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
=====================================
@@ -1,24 +1,21 @@
-Contact: last at 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
- Journal: Nucl. Acids Res.
- Volume: 38
- Number: 7
- Pages: e100
- DOI: 10.1093/nar/gkq010
- Year: 2010
- URL: http://nar.oxfordjournals.org/cgi/content/abstract/38/7/e100
- ePrint: http://nar.oxfordjournals.org/cgi/reprint/38/7/e100.pdf
- PMID: 20110255
+- Author: Frith, Martin C. and Wan, Raymond and Horton, Paul
+ Title: "Incorporating sequence quality data into alignment improves DNA read mapping\n"
+ Journal: Nucl. Acids Res.
+ Volume: 38
+ Number: 7
+ Pages: e100
+ DOI: 10.1093/nar/gkq010
+ Year: 2010
+ URL: http://nar.oxfordjournals.org/cgi/content/abstract/38/7/e100
+ ePrint: http://nar.oxfordjournals.org/cgi/reprint/38/7/e100.pdf
+ PMID: 20110255
Repository: http://last.cbrc.jp/last/
Webservice: http://lastweb.cbrc.jp/
Registry:
- - Name: OMICtools
- Entry: OMICS_15813
- - Name: bio.tools
- Entry: LAST
- - Name: SciCrunch
- Entry: SCR_006119
+- Name: OMICtools
+ Entry: OMICS_15813
+- Name: bio.tools
+ Entry: LAST
+- Name: SciCrunch
+ Entry: SCR_006119
=====================================
doc/last-dotplot.html
=====================================
@@ -498,8 +498,8 @@ strand is "+", pale blue if "-", 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 "low
-complexity" and "simple repeats", else pale red for "+" strand
-and pale blue for "-" strand.</td></tr>
+complexity", "simple repeats", and "satellites", else pale red
+for "+" strand and pale blue for "-" 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
=====================================
@@ -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
=====================================
@@ -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
=====================================
src/version.hh
=====================================
@@ -1 +1 @@
-"983"
+"984"
View it on GitLab: https://salsa.debian.org/med-team/last-align/compare/b508b3353e89cf88fe282c1e52c032e09d3be309...3bfe2036eb1069048bb6b58b570c25bb1488200f
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/compare/b508b3353e89cf88fe282c1e52c032e09d3be309...3bfe2036eb1069048bb6b58b570c25bb1488200f
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