[med-svn] [Git][med-team/last-align][upstream] New upstream version 984

[Steffen Möller]

Steffen Möller pushed to branch upstream at Debian Med / last-align


Commits:
29a2a247 by Steffen Moeller at 2019-09-04T12:05:43Z
New upstream version 984
- - - - -


5 changed files:

- ChangeLog.txt
- 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>
 


=====================================
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/commit/29a2a247153429a93415d57431a6bf7463fbfdab

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View it on GitLab: https://salsa.debian.org/med-team/last-align/commit/29a2a247153429a93415d57431a6bf7463fbfdab
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