Small script to do full variant annotation in parallel

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5853 348d0f76-0448-11de-a6fe-93d51630548a

scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala

@@ -0,0 +1,53 @@
+package oneoffs.fromer
+
+import org.broadinstitute.sting.queue.extensions.gatk._
+import org.broadinstitute.sting.queue.QScript
+import org.broadinstitute.sting.utils.interval.IntervalSetRule
+
+class ScatteredFullVariantAnnotator extends QScript {
+  qscript =>
+
+  @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. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
+  var scatterCount = 0
+
+  @Input(doc = "bam input, as .bam or as a list of files", shortName = "I", required = true)
+  var bams: File = _
+
+  @Input(doc = "variant calls to annotate", fullName = "variantVCF", shortName = "C", required = true)
+  var variantVCF: File = _
+
+  @Output(doc = "annotated file to output", shortName = "o", required = true)
+  var outputAnnotated: File = _
+
+
+  def script = {
+    add(new ScatteredFullVariantAnnotator())
+  }
+
+  trait CommandLineGATKArgs extends CommandLineGATK {
+    this.intervalsString = List(qscript.intervals)
+    this.jarFile = qscript.gatkJarFile
+    this.reference_sequence = qscript.referenceFile
+    this.input_file = List(qscript.bams)
+    this.logging_level = "INFO"
+
+    this.rodToIntervalTrackName = "variant"
+    this.BTI_merge_rule = IntervalSetRule.INTERSECTION
+  }
+
+  class ScatteredFullVariantAnnotator() extends org.broadinstitute.sting.queue.extensions.gatk.VariantAnnotator with CommandLineGATKArgs {
+    this.scatterCount = qscript.scatterCount
+    this.variantVCF = qscript.variantVCF
+    this.useAllAnnotations = true
+    this.out = qscript.outputAnnotated
+  }
+}