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Added an optional argument -bt <num_threads> for BWA to run multithreaded.

This commit is contained in:
Mauricio Carneiro 2011-06-30 14:41:57 -04:00
parent f4463d38ca
commit 197b7141c1
1 changed files with 4 additions and 2 deletions
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6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -69,6 +69,8 @@ class DataProcessingPipeline extends QScript {
@Input(doc="Decompose input BAM file and fully realign it using BWA and assume Pair Ended reads", fullName="use_bwa_pair_ended", shortName="bwape", required=false)
var useBWApe: Boolean = false
@Input(doc="Number of threads BWA should use", fullName="bwa_threads", shortName="bt", required=false)
var bwaThreads: Int = 1
/****************************************************************************
@ -433,7 +435,7 @@ class DataProcessingPipeline extends QScript {
case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with BWACommonArgs {
@Input(doc="bam file to be aligned") var bam = inBam
@Output(doc="output sai file") var sai = outSai
def commandLine = bwaPath + " aln -q 5 " + reference + " -b " + bam + " > " + sai
def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b " + bam + " > " + sai
this.analysisName = queueLogDir + outSai + ".bwa_aln_se"
this.jobName = queueLogDir + outSai + ".bwa_aln_se"
}
@ -441,7 +443,7 @@ class DataProcessingPipeline extends QScript {
case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with BWACommonArgs {
@Input(doc="bam file to be aligned") var bam = inBam
@Output(doc="output sai file for 1st mating pair") var sai = outSai1
def commandLine = bwaPath + " aln -q 5 " + reference + " -b" + index + " " + bam + " > " + sai
def commandLine = bwaPath + " aln -t " + bwaThreads + " -q 5 " + reference + " -b" + index + " " + bam + " > " + sai
this.analysisName = queueLogDir + outSai1 + ".bwa_aln_pe1"
this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
}