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Fixing 'revert' when not realigning 

RevertSam was reverting the alignment information and that was screwing up the pipeline if you didn't want to run it with BWA. Fixed.
This commit is contained in:
Mauricio Carneiro 2011-10-20 17:01:54 -04:00
parent c1329c4dde
commit d7367c152a
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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@ -149,7 +149,7 @@ 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")
@ -183,16 +183,16 @@ 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
} }
@ -212,7 +212,7 @@ class DataProcessingPipeline extends QScript {
val bams = QScriptUtils.createListFromFile(input) val bams = QScriptUtils.createListFromFile(input)
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)
@ -408,9 +408,10 @@ 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"