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Now compiles. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4295 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-16 18:49:53 +00:00
parent c581bd2d84
commit c1720cc8f5
1 changed files with 1 additions and 4 deletions
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5
scala/qscript/fullCallingPipeline.q
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@ -127,10 +127,7 @@ class fullCallingPipeline extends QScript {
// step through the un-indel-cleaned graph: // step through the un-indel-cleaned graph:
// 1a. call snps and indels // 1a. call snps and indels
val snps = new UnifiedGenotyper with CommandLineGATKArgs val snps = new UnifiedGenotyper with CommandLineGATKArgs
for ( bam <- bamFiles ) { snps.input_file = bamFiles
snps.input_file :+= bam.toNamedFile
}
//snps.input_file = bamFiles
snps.group :+= "Standard" snps.group :+= "Standard"
snps.out = new File(base+".vcf") snps.out = new File(base+".vcf")
snps.standard_min_confidence_threshold_for_emitting = Some(10) snps.standard_min_confidence_threshold_for_emitting = Some(10)