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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2012-06-26 14:55:41 -04:00
parent 7eb3e4da41 334d66f2b1
commit 9346c5b37a
1 changed files with 3 additions and 3 deletions
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6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -68,8 +68,8 @@ class DataProcessingPipeline extends QScript {
@Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false) @Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
var bwaThreads: Int = 1 var bwaThreads: Int = 1
@Input(doc="Dont perform validation on the BAM files", fullName="no_validation", shortName="nv", required=false) @Input(doc="Perform validation on the BAM files", fullName="validation", shortName="vs", required=false)
var noValidation: Boolean = false var validation: Boolean = false
/**************************************************************************** /****************************************************************************
@ -268,7 +268,7 @@ class DataProcessingPipeline extends QScript {
// Validation is an optional step for the BAM file generated after // Validation is an optional step for the BAM file generated after
// alignment and the final bam file of the pipeline. // alignment and the final bam file of the pipeline.
if (!noValidation) { if (validation) {
for (sampleFile <- bamList) for (sampleFile <- bamList)
add(validate(sampleFile, preValidateLog), add(validate(sampleFile, preValidateLog),
validate(recalBam, postValidateLog)) validate(recalBam, postValidateLog))