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Disabling indel quals in BaseRecalibrator as it should be, not PrintReads.

This commit is contained in:
Eric Banks 2012-08-01 09:23:04 -04:00
parent 79195b97a3
commit 7cf4b63d76
2 changed files with 2 additions and 2 deletions
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2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -347,6 +347,7 @@ class DataProcessingPipeline extends QScript {
this.knownSites ++= qscript.dbSNP this.knownSites ++= qscript.dbSNP
this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate") this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
this.input_file :+= inBam this.input_file :+= inBam
this.disable_indel_quals = true
this.out = outRecalFile this.out = outRecalFile
if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform
if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString) if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)
@ -359,7 +360,6 @@ class DataProcessingPipeline extends QScript {
case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs { case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs {
this.input_file :+= inBam this.input_file :+= inBam
this.BQSR = inRecalFile this.BQSR = inRecalFile
this.disable_indel_quals = true
this.baq = CalculationMode.CALCULATE_AS_NECESSARY this.baq = CalculationMode.CALCULATE_AS_NECESSARY
this.out = outBam this.out = outBam
if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString) if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString)

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -166,6 +166,7 @@ class PacbioProcessingPipeline extends QScript {
this.knownSites :+= dbSNP this.knownSites :+= dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
this.input_file :+= inBam this.input_file :+= inBam
this.disable_indel_quals = true
this.out = outRecalFile this.out = outRecalFile
this.analysisName = queueLogDir + outRecalFile + ".covariates" this.analysisName = queueLogDir + outRecalFile + ".covariates"
this.jobName = queueLogDir + outRecalFile + ".covariates" this.jobName = queueLogDir + outRecalFile + ".covariates"
@ -178,7 +179,6 @@ class PacbioProcessingPipeline extends QScript {
this.input_file :+= inBam this.input_file :+= inBam
this.BQSR = inRecalFile this.BQSR = inRecalFile
this.out = outBam this.out = outBam
this.disable_indel_quals = true
this.isIntermediate = false this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration" this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration" this.jobName = queueLogDir + outBam + ".recalibration"