From ed55182a4c5553eb517569567e5193a12eb7e68a Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sat, 16 Jul 2011 00:09:00 -0400
Subject: [PATCH] Removing Broad specific paths from parameters and making them
 required. This should make it unambiguous for people inside and outside the
 Broad to use the DataProcessingPipeline (as per request in the
 GetSatisfaction)

---
 .../qscripts/DataProcessingPipeline.scala     | 20 +++++++++----------
 1 file changed, 10 insertions(+), 10 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 050604b4e..4d4499990 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -3,10 +3,11 @@ package org.broadinstitute.sting.queue.qscripts
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 import org.broadinstitute.sting.queue.function.ListWriterFunction
+import org.broadinstitute.sting.queue.extensions.picard._
+import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
+import org.broadinstitute.sting.utils.baq.BAQ.CalculationMode
 
 import collection.JavaConversions._
-import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
-import org.broadinstitute.sting.queue.extensions.picard._
 import net.sf.samtools.SAMFileReader
 import net.sf.samtools.SAMFileHeader.SortOrder
 
@@ -29,6 +30,11 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="Reference fasta file", fullName="reference", shortName="R", required=true)
   var reference: File = _
 
+  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
+  var dbSNP: File = _
+
+  @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=true)
+  var indels: File = _
 
 
   /****************************************************************************
@@ -42,12 +48,6 @@ class DataProcessingPipeline extends QScript {
   @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
   var bwaPath: File = _
 
-  @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=false)
-  var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
-
-  @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
-  var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
-
   @Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
   var projectName: String = "project"
 
@@ -295,7 +295,7 @@ class DataProcessingPipeline extends QScript {
     this.targetIntervals = tIntervals
     this.out = outBam
     this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
-    this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
+    this.rodBind :+= RodBind("indels", "VCF", indels)
     this.consensusDeterminationModel =  consensusDeterminationModel
     this.compress = 0
     this.scatterCount = nContigs
@@ -318,7 +318,7 @@ class DataProcessingPipeline extends QScript {
   case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
     this.input_file :+= inBam
     this.recal_file = inRecalFile
-    this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
+    this.baq = CalculationMode.CALCULATE_AS_NECESSARY
     this.out = outBam
     if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
     else if (qscript.intervals != null) this.intervals :+= qscript.intervals