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 2011-07-16 00:23:59 -04:00
parent 2fa5dbb0fe dd92a14b40
commit 5cb5a4ec75
1 changed files with 8 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -33,10 +33,6 @@ class DataProcessingPipeline extends QScript {
@Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
var dbSNP: File = _
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=true)
var indels: File = _
/****************************************************************************
* Optional Parameters
****************************************************************************/
@ -45,6 +41,10 @@ class DataProcessingPipeline extends QScript {
// @Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
// var sortSamJar: File = _
//
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
var indels: File = _
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
var bwaPath: File = _
@ -288,7 +288,8 @@ class DataProcessingPipeline extends QScript {
this.out = outIntervals
this.mismatchFraction = 0.0
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", indels)
if (!indels.isEmpty)
this.rodBind :+= RodBind("indels", "VCF", indels)
this.scatterCount = nContigs
this.analysisName = queueLogDir + outIntervals + ".target"
this.jobName = queueLogDir + outIntervals + ".target"
@ -299,7 +300,8 @@ class DataProcessingPipeline extends QScript {
this.targetIntervals = tIntervals
this.out = outBam
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", indels)
if (!indels.isEmpty)
this.rodBind :+= RodBind("indels", "VCF", indels)
this.consensusDeterminationModel = consensusDeterminationModel
this.compress = 0
this.scatterCount = nContigs