zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-30 02:06:45 -04:00
parent b06deac9ea 2d94037ad0
commit e7b4959ebe
1 changed files with 4 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -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