From c0d4110ffd2ccf75e28866d9b6f5b98161683148 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Fri, 29 Jul 2011 10:01:11 -0400 Subject: [PATCH 1/2] Correcting redundant warning text. --- .../genotyper/SNPGenotypeLikelihoodsCalculationModel.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java index 3e3cd128b..9d917078d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java @@ -68,7 +68,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC if ( vc == null ) { vc = vc_input; } else { - logger.warn("Multiple valid VCF records detected at site " + ref.getLocus() + ", only considering alleles from first record only"); + logger.warn("Multiple valid VCF records detected at site " + ref.getLocus() + ", only considering alleles from first record"); } } } From 2d94037ad06e3cf2b7b3a78f700b52a58c280d82 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Sat, 30 Jul 2011 02:05:22 -0400 Subject: [PATCH 2/2] Remove temporary index files (*.bai) some temporary index files were not being removed. --- .../sting/queue/qscripts/DataProcessingPipeline.scala | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index 1f4f79993..959d073c7 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -365,6 +365,7 @@ class DataProcessingPipeline extends QScript { } case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs { + @Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai") this.input = List(inBam) this.output = outBam this.metrics = metricsFile @@ -373,6 +374,7 @@ class DataProcessingPipeline extends QScript { } case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles with ExternalCommonArgs { + @Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai") this.input = inBams this.output = outBam this.analysisName = queueLogDir + outBam + ".joinBams" @@ -380,6 +382,7 @@ class DataProcessingPipeline extends QScript { } case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam with ExternalCommonArgs { + @Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai") this.input = List(inSam) this.output = outBam this.sortOrder = sortOrderP @@ -399,6 +402,7 @@ class DataProcessingPipeline extends QScript { case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs { + @Output(doc="output bai file") var bai = swapExt(outBam, ".bam", ".bai") this.input = List(inBam) this.output = outBam this.RGID = readGroup.id