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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-16 00:15:19 -04:00
parent 43bd45fcad ed55182a4c
commit 2fa5dbb0fe
1 changed files with 10 additions and 10 deletions
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20
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -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"
@ -299,7 +299,7 @@ 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
@ -322,7 +322,7 @@ 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