From a93a9ac663d582270f44072ac398d5829f0dd908 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 2 May 2011 16:29:11 +0000
Subject: [PATCH] adding gold standard (full coverage) to the variant eval
 analysis output.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5721 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/oneoffs/carneiro/downsampling.scala | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scala/qscript/oneoffs/carneiro/downsampling.scala b/scala/qscript/oneoffs/carneiro/downsampling.scala
index fcb0a8dc9..2b000f94a 100644
--- a/scala/qscript/oneoffs/carneiro/downsampling.scala
+++ b/scala/qscript/oneoffs/carneiro/downsampling.scala
@@ -54,6 +54,7 @@ class downsampling extends QScript {
 
   val queueLogDir: String = ".qlog/"
   val outFile: String = "cov.out"
+  val fullCoverageVCF = new File("/humgen/gsa-hpprojects/dev/carneiro/downsampling/analysis/fullcov/fullcov.F1.filtered.vcf")
 
   def script = {
     val nIntervals = math.min(200, countLines(targetIntervals))
@@ -126,6 +127,7 @@ class downsampling extends QScript {
     this.stratificationModule ++= List("EvalRod", "CompRod", "Novelty")
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
     this.rodBind :+= RodBind("eval", "VCF", inFile)
+    this.rodBind :+= RodBind("comp", "VCF", fullCoverageVCF)
     this.out = outFile
     this.analysisName = outFile + "_VariantEval"
     this.jobName = queueLogDir + outFile