From 3c1a026c94c44eb0f6f110e00016d71cbee0bb35 Mon Sep 17 00:00:00 2001 From: fromer Date: Mon, 7 Feb 2011 16:47:55 +0000 Subject: [PATCH] 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 --- .../qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala b/scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala index 1ad620a31..1b6b81eec 100644 --- a/scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala +++ b/scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala @@ -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