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Reverting the DPP to the original version, going to create a new simplified version for CMI in private.

This commit is contained in:
Mauricio Carneiro 2012-09-25 12:02:34 -04:00
parent 4324bd72fd
commit 65b100f9b0
1 changed files with 8 additions and 12 deletions
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20
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -96,7 +96,6 @@ class DataProcessingPipeline extends QScript {
var cleanModelEnum: ConsensusDeterminationModel = ConsensusDeterminationModel.USE_READS
val bwaParameters: String = " -q 5 -l 32 -k 2 -t 4 -o 1 "
@ -166,15 +165,12 @@ class DataProcessingPipeline extends QScript {
var realignedBams: Seq[File] = Seq()
var index = 1
for (bam <- bams) {
val extension = bam.toString.substring(bam.toString.length - 4)
val saiFile1 = swapExt(bam, extension, "." + index + ".1.sai")
val saiFile2 = swapExt(bam, extension, "." + index + ".2.sai")
val realignedSamFile = swapExt(bam, extension, "." + index + ".realigned.sam")
val realignedBamFile = swapExt(bam, extension, "." + index + ".realigned.bam")
val rgRealignedBamFile = swapExt(bam, extension, "." + index + ".realigned.rg.bam")
// first revert the BAM file to the original qualities
val saiFile1 = swapExt(bam, ".bam", "." + index + ".1.sai")
val saiFile2 = swapExt(bam, ".bam", "." + index + ".2.sai")
val realignedSamFile = swapExt(bam, ".bam", "." + index + ".realigned.sam")
val realignedBamFile = swapExt(bam, ".bam", "." + index + ".realigned.bam")
val rgRealignedBamFile = swapExt(bam, ".bam", "." + index + ".realigned.rg.bam")
if (useBWAse) {
val revertedBAM = revertBAM(bam, true)
@ -448,7 +444,7 @@ class DataProcessingPipeline extends QScript {
case class bwa_aln_se (inBam: File, outSai: File) extends CommandLineFunction with ExternalCommonArgs {
@Input(doc="bam file to be aligned") var bam = inBam
@Output(doc="output sai file") var sai = outSai
def commandLine = bwaPath + " aln -t " + bwaThreads + bwaParameters + 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"
}
@ -456,7 +452,7 @@ class DataProcessingPipeline extends QScript {
case class bwa_aln_pe (inBam: File, outSai1: File, index: Int) extends CommandLineFunction with ExternalCommonArgs {
@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 -t " + bwaThreads + bwaParameters + 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"
}