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gatk-3.8
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+ Added override to extractFileEntries 

+ UG now doesn't care whether it's given SNPs or indels to genotype, it will do the right thing -- so remove the option to specify which GM user wants

+ Max misamatches argument removed

integration test will follow



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5638 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-04-14 15:13:35 +00:00
parent cad6722cf6
commit 47fa7e2227
1 changed files with 1 additions and 7 deletions
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8
scala/qscript/playground/BatchMerge.q
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@ -22,9 +22,7 @@ class batchMergePipeline extends QScript {
//@Argument(doc="read UG settings from header",shortName="ugh") var ugSettingsFromHeader : Boolean = false
@Hidden @Argument(doc="Min base q",shortName="mbq",required=false) var mbq : Int = 20
@Hidden @Argument(doc="Min map q",shortName="mmq",required=false) var mmq : Int = 20
@Hidden @Argument(doc="Max mismatching bases",shortName="mmb",required=false) var mmb : Int = 3
@Hidden @Argument(doc="baq gap open penalty, using sets baq to calc when necessary",shortName="baqp",required=false) var baq : Int = -1
@Hidden @Argument(doc="VCFs are indels",shortName="indel") var indelMode : Boolean = false
def script = {
@ -48,7 +46,6 @@ class batchMergePipeline extends QScript {
trait CalcLikelihoodArgs extends UGCalcLikelihoods {
this.reference_sequence = batchMerge.ref
this.max_mismatches_in_40bp_window = batchMerge.mmb
this.min_base_quality_score = batchMerge.mbq
this.min_mapping_quality_score = batchMerge.mmq
if ( batchMerge.baq >= 0 ) {
@ -62,9 +59,6 @@ class batchMergePipeline extends QScript {
this.scatterCount = 60
this.output_mode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES
this.genotyping_mode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
if ( batchMerge.indelMode ) {
this.genotype_likelihoods_model = GenotypeLikelihoodsCalculationModel.Model.DINDEL
}
}
def newUGCL( bams: (List[File],Int) ) : UGCalcLikelihoods = {
@ -110,7 +104,7 @@ class batchMergePipeline extends QScript {
add(combine)
}
def extractFileEntries(in: File): List[File] = {
override def extractFileEntries(in: File): List[File] = {
return (new XReadLines(in)).readLines.toList.map( new File(_) )
}
}