Preliminary Qscript to run DoC for the purpose of CNV detection

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5194 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala

@@ -0,0 +1,64 @@
+package oneoffs.fromer
+
+import org.broadinstitute.sting.queue.extensions.gatk._
+import org.broadinstitute.sting.queue.QScript
+
+import org.broadinstitute.sting.gatk.DownsampleType
+
+
+class ReadDepthCNVanalysis extends QScript {
+  qscript =>
+
+  @Input(doc = "bam input, as .bam or as a list of files", shortName = "I", required = true)
+  var bams: File = _
+
+  @Argument(doc = "gatk jar file", shortName = "J", required = true)
+  var gatkJarFile: File = _
+
+  @Argument(shortName = "R", doc = "ref", required = true)
+  var referenceFile: File = _
+
+  @Argument(shortName = "L", doc = "Intervals", required = false)
+  var intervals: String = _
+
+  @Input(doc = "level of parallelism for BAM DoC.   By default is set to 0 [no scattering].", shortName = "scatter", required = false)
+  var scatterCountInput = 0
+
+  @Output(doc = "DoC file to output", shortName = "o", required = true)
+  var outputDoC: File = _
+
+  @Input(doc = "Maximum depth (before GATK down-sampling kicks in...)", shortName = "MAX_DEPTH", required = false)
+  var MAX_DEPTH = 20000
+
+  trait CommandLineGATKArgs extends CommandLineGATK {
+    this.intervalsString = List(qscript.intervals)
+    this.jarFile = qscript.gatkJarFile
+    this.reference_sequence = qscript.referenceFile
+    this.memoryLimit = Some(3)
+    this.logging_level = "INFO"
+  }
+
+  def script = {
+    add(new DepthOfCoverage(bams, outputDoC))
+  }
+
+  class DepthOfCoverage(bam: File, docOutPath: File) extends org.broadinstitute.sting.queue.extensions.gatk.DepthOfCoverage with CommandLineGATKArgs {
+    this.omitIntervalStatistics = false
+    this.omitDepthOutputAtEachBase = true
+    this.omitLocusTable = true
+
+    this.minBaseQuality = Some(0)
+    this.minMappingQuality = Some(0)
+
+    this.out = docOutPath
+    this.input_file :+= bam
+
+    this.dcov = Some(MAX_DEPTH)
+    this.downsampling_type = Some(DownsampleType.BY_SAMPLE)
+
+    this.scatterCount = scatterCountInput
+
+    override def dotString = "DOC: " + bam.getName
+  }
+
+}