v4.0.0 - BigWig files for GenomeBrowsers

Now generates 7 additional files by default:

X.copynumber.baf.bw
X.copynumber.logR.bw
X.copynumber.minorCn.bw
X.copynumber.rawCn.bw
X.copynumber.segBaf.bw
X.copynumber.segLogR.bw
X.copynumber.totalCn.bw

This behaviour is optional (and requires cgpBigWig). To disable add -nb to your command.

JBrowse example displays:

LogR

BAF

CN

JBrowse config
Using the MultiBigWig plugin:

{
  "storeClass" : "MultiBigWig/Store/SeqFeature/MultiBigWig",
  "max_score" : 1,
  "min_score" : -1,
  "style": { "height": 100 },
  "urlTemplates" : [
    {"url":"ascat/X.copynumber.logR.bw","name":"logR", "color": "grey", "nonCont": true},
    {"url":"ascat/X.copynumber.segLogR.bw","name":"segLogR", "color": "green", "nonCont": true}
  ],
  "showTooltips": true,
  "label" : "ascatLogR",
  "type" : "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
},
{
  "storeClass" : "MultiBigWig/Store/SeqFeature/MultiBigWig",
  "max_score" : 1,
  "min_score" : 0,
  "style": { "height": 100 },
  "urlTemplates" : [
    {"url":"ascat/X.copynumber.baf.bw","name":"BAF", "color": "grey", "nonCont": true},
    {"url":"ascat/X.copynumber.segBaf.bw","name":"segBAF", "color": "green", "nonCont": true}
  ],
  "showTooltips": true,
  "label" : "ascatBAF",
  "type" : "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
},
{
  "storeClass" : "MultiBigWig/Store/SeqFeature/MultiBigWig",
  "max_score" : 10,
  "min_score" : 0,
  "style": { "height": 100 },
  "urlTemplates" : [
    {"url":"ascat/X.copynumber.rawCn.bw","name":"rawCn", "color": "grey", "nonCont": true},
    {"url":"ascat/X.copynumber.totalCn.bw","name":"totalCn", "color": "green", "nonCont": true},
    {"url":"ascat/X.copynumber.minorCn.bw","name":"minorCn", "color": "red", "nonCont": true},
  ],
  "showTooltips": true,
  "label" : "ascatCn",
  "type" : "MultiBigWig/View/Track/MultiWiggle/MultiXYPlot"
}