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Updating validation parameter in the DPP 

users were very confused with the failing validation of their 'unpicarded' bam files. Changed the default to OFF and added an option to turn it on.
This commit is contained in:
Mauricio Carneiro 2012-06-26 14:54:37 -04:00
parent 3b2fab9a37
commit 334d66f2b1
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)
var bwaThreads: Int = 1
@Input(doc="Dont perform validation on the BAM files", fullName="no_validation", shortName="nv", required=false)
var noValidation: Boolean = false
@Input(doc="Perform validation on the BAM files", fullName="validation", shortName="vs", required=false)
var validation: Boolean = false
/****************************************************************************
@ -268,7 +268,7 @@ class DataProcessingPipeline extends QScript {
// Validation is an optional step for the BAM file generated after
// alignment and the final bam file of the pipeline.
if (!noValidation) {
if (validation) {
for (sampleFile <- bamList)
add(validate(sampleFile, preValidateLog),
validate(recalBam, postValidateLog))