From c581bd2d84b73d6ad2726559d344788fac5f991e Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 16 Sep 2010 18:29:24 +0000 Subject: [PATCH] Minor modifications to fCP git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4294 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/fullCallingPipeline.q | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index e3ab08822..1ffb04f81 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -127,7 +127,10 @@ class fullCallingPipeline extends QScript { // step through the un-indel-cleaned graph: // 1a. call snps and indels val snps = new UnifiedGenotyper with CommandLineGATKArgs - snps.input_file = bamFiles + for ( bam <- bamFiles ) { + snps.input_file :+= bam.toNamedFile + } + //snps.input_file = bamFiles snps.group :+= "Standard" snps.out = new File(base+".vcf") snps.standard_min_confidence_threshold_for_emitting = Some(10) @@ -157,7 +160,7 @@ class fullCallingPipeline extends QScript { var loopNo = 0 var priority = "" for ( bam <- bamFiles ) { - val indel = new IndelGenotyperV2 with CommandLineGATKArgs + var indel = new IndelGenotyperV2 with CommandLineGATKArgs indel.input_file :+= bam indel.out = swapExt(bam,".bam",".indels.vcf") indel.downsample_to_coverage = Some(500)