Commit 29a2a247 authored by Steffen Möller's avatar Steffen Möller
Browse files

New upstream version 984

parent 3a17cb1f

ChangeLog.txt

+7 −1
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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

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@@ -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

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@@ -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

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@@ -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

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"983"
 
"984"