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Updated script to properly bin DoC values so that down-sampling corresponds to range of DoC values obtainable 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5208 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-02-07 16:47:55 +00:00
parent 698096dc5a
commit 3c1a026c94
1 changed files with 10 additions and 0 deletions
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10
scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala
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@ -30,6 +30,12 @@ class ReadDepthCNVanalysis extends QScript {
@Input(doc = "Maximum depth (before GATK down-sampling kicks in...)", shortName = "MAX_DEPTH", required = false)
var MAX_DEPTH = 20000
@Input(doc = "Number of read-depth bins", shortName = "NUM_BINS", required = false)
var NUM_BINS = 200
@Input(doc = "Starting value of read-depth bins", shortName = "START_BIN", required = false)
var START_BIN = 1
trait CommandLineGATKArgs extends CommandLineGATK {
this.intervalsString = List(qscript.intervals)
this.jarFile = qscript.gatkJarFile
@ -56,6 +62,10 @@ class ReadDepthCNVanalysis extends QScript {
this.dcov = Some(MAX_DEPTH)
this.downsampling_type = Some(DownsampleType.BY_SAMPLE)
this.start = Some(START_BIN)
this.stop = Some(MAX_DEPTH)
this.nBins = Some(NUM_BINS)
this.scatterCount = scatterCountInput
override def dotString = "DOC: " + bam.getName