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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-08-01 11:23:18 -04:00
parent 33b32c4211 e7b4959ebe
commit 3a9b6eacdf
2 changed files with 5 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -68,7 +68,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
if ( vc == null ) { if ( vc == null ) {
vc = vc_input; vc = vc_input;
} else { } 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");
} }
} }
} }

4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -365,6 +365,7 @@ class DataProcessingPipeline extends QScript {
} }
case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs { 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.input = List(inBam)
this.output = outBam this.output = outBam
this.metrics = metricsFile this.metrics = metricsFile
@ -373,6 +374,7 @@ class DataProcessingPipeline extends QScript {
} }
case class joinBams (inBams: List[File], outBam: File) extends MergeSamFiles with ExternalCommonArgs { 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.input = inBams
this.output = outBam this.output = outBam
this.analysisName = queueLogDir + outBam + ".joinBams" 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 { 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.input = List(inSam)
this.output = outBam this.output = outBam
this.sortOrder = sortOrderP this.sortOrder = sortOrderP
@ -399,6 +402,7 @@ class DataProcessingPipeline extends QScript {
case class addReadGroup (inBam: File, outBam: File, readGroup: ReadGroup) extends AddOrReplaceReadGroups with ExternalCommonArgs { 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.input = List(inBam)
this.output = outBam this.output = outBam
this.RGID = readGroup.id this.RGID = readGroup.id