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Fixing a silly typo 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4680 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-11-15 18:16:51 +00:00
parent a64f693b20
commit 5466365575
1 changed files with 2 additions and 2 deletions
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4
scala/qscript/fullCallingPipeline.q
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@ -213,7 +213,7 @@ class fullCallingPipeline extends QScript {
snps.min_base_quality_score = Some(20) snps.min_base_quality_score = Some(20)
snps.downsample_to_coverage = Some(qscript.downsampling_coverage) snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
//snps.annotation :+= "QualByDepthV2" //snps.annotation :+= "QualByDepthV2"
snps.dbsnp =qscript.pipeline.getProject.getDbsnpFile snps.DBSNP = qscript.pipeline.getProject.getDbsnpFile
//if (qscript.trigger != null) { //if (qscript.trigger != null) {
// snps.trigger_min_confidence_threshold_for_calling = Some(30) // snps.trigger_min_confidence_threshold_for_calling = Some(30)
@ -323,7 +323,7 @@ class fullCallingPipeline extends QScript {
clusters.DBSNP = qscript.pipeline.getProject.getDbsnpFile clusters.DBSNP = qscript.pipeline.getProject.getDbsnpFile
val clusters_clusterFile = swapExt("SnpCalls/IntermediateFiles",snps.out,".vcf",".cluster") val clusters_clusterFile = swapExt("SnpCalls/IntermediateFiles",snps.out,".vcf",".cluster")
clusters.clusterFile = clusters_clusterFile clusters.clusterFile = clusters_clusterFile
clusters.memoryLimit = Some(6) clusters.memoryLimit = Some(4)
clusters.jobQueue = qscript.big_mem_queue clusters.jobQueue = qscript.big_mem_queue
clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")