From caebc88e9a75f63c1638419e7747f576af6308cc Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 22 Aug 2011 14:05:13 -0400
Subject: [PATCH] Consensus mode and new RodBinding framework.

The DPP was not using the parameter correctly. It didn't matter for the default option (which is the only one we have been testing) but it would not work for knowns only or smith waterman. It is fixed now.

It now complies with the new rod binding framework.
---
 .../qscripts/DataProcessingPipeline.scala     | 32 +++++++++++--------
 1 file changed, 19 insertions(+), 13 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index 47ba0220f..03d1d7766 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -84,12 +84,6 @@ class DataProcessingPipeline extends QScript {
   var nContigs: Int = 0               // Use the number of contigs for scatter gathering jobs
   var cleanModelEnum: ConsensusDeterminationModel = ConsensusDeterminationModel.USE_READS
 
-  if (cleaningModel == "KNOWNS_ONLY")  {
-    cleanModelEnum = ConsensusDeterminationModel.KNOWNS_ONLY
-  }
-  else if (cleaningModel == "USE_SW") {
-    cleanModelEnum = ConsensusDeterminationModel.USE_SW
-  }
 
 
 
@@ -200,6 +194,15 @@ class DataProcessingPipeline extends QScript {
     return realignedBams
   }
 
+  def getIndelCleaningModel(): ConsensusDeterminationModel = {
+    if (cleaningModel == "KNOWNS_ONLY")
+      ConsensusDeterminationModel.KNOWNS_ONLY
+    else if (cleaningModel == "USE_SW")
+      ConsensusDeterminationModel.USE_SW
+    else
+      ConsensusDeterminationModel.USE_READS
+  }
+
 
   /****************************************************************************
   * Main script
@@ -208,6 +211,8 @@ class DataProcessingPipeline extends QScript {
 
   def script = {
 
+    cleanModelEnum = getIndelCleaningModel()
+
     // keep a record of the number of contigs in the first bam file in the list
     val bams = QScriptUtils.createListFromFile(input)
     nContigs = QScriptUtils.getNumberOfContigs(bams(0))
@@ -300,13 +305,13 @@ class DataProcessingPipeline extends QScript {
   }
 
   case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
-    if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
+    if (cleanModelEnum != ConsensusDeterminationModel.KNOWNS_ONLY)
       this.input_file :+= inBams
     this.out = outIntervals
     this.mismatchFraction = 0.0
-    this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    this.known :+= qscript.dbSNP
     if (indels != null)
-      this.rodBind :+= RodBind("indels", "VCF", indels)
+      this.known :+= qscript.indels
     this.scatterCount = nContigs
     this.analysisName = queueLogDir + outIntervals + ".target"
     this.jobName = queueLogDir + outIntervals + ".target"
@@ -317,10 +322,10 @@ class DataProcessingPipeline extends QScript {
     this.input_file :+= inBams
     this.targetIntervals = tIntervals
     this.out = outBam
-    this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    this.known :+= qscript.dbSNP
     if (qscript.indels != null)
-      this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
-    this.consensusDeterminationModel =  consensusDeterminationModel
+      this.known :+= qscript.indels
+    this.consensusDeterminationModel = cleanModelEnum
     this.compress = 0
     this.scatterCount = nContigs
     this.analysisName = queueLogDir + outBam + ".clean"
@@ -328,7 +333,7 @@ class DataProcessingPipeline extends QScript {
   }
 
   case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
-    this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
+    this.knownSites :+= qscript.dbSNP
     this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
     this.input_file :+= inBam
     this.recal_file = outRecalFile
@@ -372,6 +377,7 @@ class DataProcessingPipeline extends QScript {
     this.input = List(inBam)
     this.output = outBam
     this.metrics = metricsFile
+    this.memoryLimit = 16
     this.analysisName = queueLogDir + outBam + ".dedup"
     this.jobName = queueLogDir + outBam + ".dedup"
   }