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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-10-20 17:03:22 -04:00
parent 558a7a81f0 d7367c152a
commit 093cd95c5d
1 changed files with 8 additions and 7 deletions
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15
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -162,7 +162,7 @@ class DataProcessingPipeline extends QScript {
var index = 1 var index = 1
for (bam <- bams) { for (bam <- bams) {
// first revert the BAM file to the original qualities // first revert the BAM file to the original qualities
val revertedBAM = revertBAM(bam) val revertedBAM = revertBAM(bam, true)
val readSortedBam = swapExt(revertedBAM, ".bam", "." + index + ".sorted.bam" ) val readSortedBam = swapExt(revertedBAM, ".bam", "." + index + ".sorted.bam" )
val saiFile1 = swapExt(bam, ".bam", "." + index + ".1.sai") val saiFile1 = swapExt(bam, ".bam", "." + index + ".1.sai")
val saiFile2 = swapExt(bam, ".bam", "." + index + ".2.sai") val saiFile2 = swapExt(bam, ".bam", "." + index + ".2.sai")
@ -196,16 +196,16 @@ class DataProcessingPipeline extends QScript {
ConsensusDeterminationModel.USE_READS ConsensusDeterminationModel.USE_READS
} }
def revertBams(bams: List[File]): List[File] = { def revertBams(bams: List[File], removeAlignmentInformation: Boolean): List[File] = {
var revertedBAMList: List[File] = List() var revertedBAMList: List[File] = List()
for (bam <- bams) for (bam <- bams)
revertedBAMList :+= revertBAM(bam) revertedBAMList :+= revertBAM(bam, removeAlignmentInformation)
return revertedBAMList return revertedBAMList
} }
def revertBAM(bam: File): File = { def revertBAM(bam: File, removeAlignmentInformation: Boolean): File = {
val revertedBAM = swapExt(bam, ".bam", ".reverted.bam") val revertedBAM = swapExt(bam, ".bam", ".reverted.bam")
add(revert(bam, revertedBAM)) add(revert(bam, revertedBAM, removeAlignmentInformation))
return revertedBAM return revertedBAM
} }
@ -226,7 +226,7 @@ class DataProcessingPipeline extends QScript {
if (nContigs < 0) if (nContigs < 0)
nContigs = QScriptUtils.getNumberOfContigs(bams(0)) nContigs = QScriptUtils.getNumberOfContigs(bams(0))
val realignedBAMs = if (useBWApe || useBWAse) {performAlignment(bams)} else {revertBams(bams)} val realignedBAMs = if (useBWApe || useBWAse) {performAlignment(bams)} else {revertBams(bams, false)}
// generate a BAM file per sample joining all per lane files if necessary // generate a BAM file per sample joining all per lane files if necessary
val sampleBAMFiles: Map[String, List[File]] = createSampleFiles(bams, realignedBAMs) val sampleBAMFiles: Map[String, List[File]] = createSampleFiles(bams, realignedBAMs)
@ -423,9 +423,10 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".rg" this.jobName = queueLogDir + outBam + ".rg"
} }
case class revert (inBam: File, outBam: File) extends RevertSam with ExternalCommonArgs { case class revert (inBam: File, outBam: File, removeAlignmentInfo: Boolean) extends RevertSam with ExternalCommonArgs {
this.output = outBam this.output = outBam
this.input :+= inBam this.input :+= inBam
this.removeAlignmentInformation = removeAlignmentInfo;
this.analysisName = queueLogDir + outBam + "revert" this.analysisName = queueLogDir + outBam + "revert"
this.jobName = queueLogDir + outBam + ".revert" this.jobName = queueLogDir + outBam + ".revert"