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One more little bfix -- the issue was not the grep command, but instead the NFS in the awk; i changed it to ++count in the last commit which was really responsible for the fix. Then this ultra-escaping semi-broke teh grep again. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4831 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-12-13 20:36:14 +00:00
parent a5008faca8
commit f36861eeee
2 changed files with 9 additions and 4 deletions
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11
scala/qscript/chartl/private_mutations.q
View File

@ -11,6 +11,7 @@ class private_mutations extends QScript {
@Argument(shortName="yaml",fullName="eomiYaml",doc="Project YAML file",required=true) var eomiYaml: File = _
@Argument(shortName="sting",fullName="stingDir",doc="path to the Sting directory",required=true) var sting: String = _
@Argument(shortName="out",fullName="finalVCF",doc="the merged vcf to write to", required=true) var finalMergedVCF : File = _
@Argument(shortName="mask",fullName="indelAndSVMask",doc="The indel/SV mask to apply during filtration",required=true) var filtMask : File = _
var gatkjar : File = _
def script = {
@ -33,6 +34,8 @@ class private_mutations extends QScript {
addAll(genotypers)
var handFilters : List[VariantFiltration] = genotypers.map( g => vcLib.StandardHandfilter(g.out,swapExt(g.out,".raw.vcf",".handfiltered.vcf")))
handFilters.foreach( p => { p.rodBind :+= new RodBind("mask","bed",filtMask)
p.mask = "NearIndelOrSV"} )
addAll(handFilters)
@ -60,7 +63,7 @@ class private_mutations extends QScript {
eval_all.out = swapExt(finalMergedVCF,".vcf",".perm.csv")
eval_all.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV)
add(eval_all)
//add(eval_all)
var eval_afr : VariantEval = vcLib.addTrait(new VariantEval)
eval_afr.rodBind :+= new RodBind("evalAFR","VCF",extract_afr.outputVCF)
@ -68,8 +71,9 @@ class private_mutations extends QScript {
eval_afr.E :+= "PrivatePermutations"
eval_afr.out = swapExt(extract_afr.outputVCF,".vcf",".perm.csv")
eval_afr.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV)
eval_afr.noStandard = true
add(eval_afr)
//add(eval_afr)
var eval_eur : VariantEval = vcLib.addTrait(new VariantEval)
eval_eur.rodBind :+= new RodBind("compAFR","VCF",extract_afr.outputVCF)
@ -77,8 +81,9 @@ class private_mutations extends QScript {
eval_eur.E :+= "PrivatePermutations"
eval_eur.out = swapExt(extract_eur.outputVCF,".vcf",".perm.csv")
eval_eur.reportType = Some(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV)
eval_eur.noStandard = true
add(eval_eur)
//add(eval_eur)
}
}

2
scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala
View File

@ -17,7 +17,7 @@ class VCFExtractSamples(inVCF: File, outVCF: File, samples: List[String]) extend
override def freezeFieldValues = {
this.logger.warn("Note: Using VCFExtractSamples invalidates AC/AF/AN annotations. This is an explicit warning.")
sampleGrep = "\"" + sampleList.reduceLeft(_ + "\\\\\\\\|" + _) + "\""
sampleGrep = "'" + sampleList.reduceLeft(_ + "|" + _) + "'"
super.freezeFieldValues
}