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fixing the pipeline so that it still works while I'm adding support for BWA. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5921 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-06-02 19:32:28 +00:00
parent 3302a733ef
commit 355be57539
1 changed files with 7 additions and 12 deletions
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19
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
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@ -9,8 +9,6 @@ import net.sf.samtools.{SAMFileReader,SAMReadGroupRecord}
import scala.io.Source._ import scala.io.Source._
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.queue.function.scattergather.ScatterFunction
import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter
class dataProcessingV2 extends QScript { class dataProcessingV2 extends QScript {
@ -106,7 +104,7 @@ class dataProcessingV2 extends QScript {
/**************************************************************************** /****************************************************************************
* Helper functions * Helper classes and methods
****************************************************************************/ ****************************************************************************/
@ -163,7 +161,7 @@ class dataProcessingV2 extends QScript {
return samReader.getFileHeader.getSequenceDictionary.getSequences.size() return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
} }
// Rebuilds the Read Group string to give BWA
def buildReadGroupString(samReader: SAMFileReader): String = { def buildReadGroupString(samReader: SAMFileReader): String = {
val readGroups = samReader.getFileHeader.getReadGroups val readGroups = samReader.getFileHeader.getReadGroups
var s = "" var s = ""
@ -183,14 +181,14 @@ class dataProcessingV2 extends QScript {
// Takes a list of processed BAM files and realign them using the BWA option requested (bwase or bwape). // Takes a list of processed BAM files and realign them using the BWA option requested (bwase or bwape).
// Returns a list of realigned BAM files. // Returns a list of realigned BAM files.
def performAlignment(bamMap: Map[String, File]) { def performAlignment(sampleBams: Map[String, File]) {
for (key <- bamMap.keysIterator) { for (key <- sampleBams.keysIterator) {
val bam: File = bamMap(key) val bam: File = sampleBams(key)
val saiFile1 = swapExt(bam, ".bam", "1.sai") val saiFile1 = swapExt(bam, ".bam", "1.sai")
val saiFile2 = swapExt(bam, ".bam", "2.sai") val saiFile2 = swapExt(bam, ".bam", "2.sai")
val realignedSamFile = swapExt(bam, ".bam", ".realigned.sam") val realignedSamFile = swapExt(bam, ".bam", ".realigned.sam")
val realignedBamFile = swapExt(bam, ".bam", ".realigned.bam") val realignedBamFile = swapExt(bam, ".bam", ".realigned.bam")
val readGroupString: String = buildReadGroupString(new SAMFileReader()) val readGroupString: String = buildReadGroupString(new SAMFileReader(bam))
if (useBWAse) { if (useBWAse) {
add(bwa_aln_se(bam, saiFile1), add(bwa_aln_se(bam, saiFile1),
bwa_sam_se(bam, saiFile1, realignedSamFile, readGroupString), bwa_sam_se(bam, saiFile1, realignedSamFile, readGroupString),
@ -202,7 +200,7 @@ class dataProcessingV2 extends QScript {
bwa_sam_pe(bam, saiFile1, saiFile2, realignedSamFile, readGroupString), bwa_sam_pe(bam, saiFile1, saiFile2, realignedSamFile, readGroupString),
to_bam(realignedSamFile, realignedBamFile)) to_bam(realignedSamFile, realignedBamFile))
} }
bamMap(key) = realignedBamFile sampleBams(key) = realignedBamFile
} }
} }
@ -231,7 +229,6 @@ class dataProcessingV2 extends QScript {
// 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, File] = createSampleFiles(bams) val sampleBamFiles: Map[String, File] = createSampleFiles(bams)
//todo -- (option - BWA) run BWA on each bam file (per lane bam file) before performing per sample processing
if (useBWApe || useBWAse) { if (useBWApe || useBWAse) {
performAlignment(sampleBamFiles) performAlignment(sampleBamFiles)
} }
@ -328,7 +325,6 @@ class dataProcessingV2 extends QScript {
this.useOnlyKnownIndels = knownsOnly this.useOnlyKnownIndels = knownsOnly
this.doNotUseSW = !useSW this.doNotUseSW = !useSW
this.compress = 0 this.compress = 0
// this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.scatterCount = nContigs this.scatterCount = nContigs
this.analysisName = queueLogDir + outBam + ".clean" this.analysisName = queueLogDir + outBam + ".clean"
this.jobName = queueLogDir + outBam + ".clean" this.jobName = queueLogDir + outBam + ".clean"
@ -353,7 +349,6 @@ class dataProcessingV2 extends QScript {
this.out = outBam this.out = outBam
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString) if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals else if (qscript.intervals != null) this.intervals :+= qscript.intervals
// this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.scatterCount = nContigs this.scatterCount = nContigs
this.isIntermediate = false this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration" this.analysisName = queueLogDir + outBam + ".recalibration"