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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-06-30 15:04:30 -04:00
parent 57806d514a 867056af51
commit b17ed7e504
2 changed files with 15 additions and 10 deletions
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2
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
View File

@ -60,7 +60,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
" --NO_HEADER" +
" -o %s",
1,
Arrays.asList("2cae3d16f9ed00b07d87e9c49272d877")
Arrays.asList("995c07ccd593fe1c35d0d28155112a55")
);
executeTest("testSimpleVCFStreaming", spec);

23
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -4,12 +4,12 @@ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.function.ListWriterFunction
import net.sf.samtools.{SAMFileReader,SAMReadGroupRecord}
import scala.io.Source._
import collection.JavaConversions._
import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
import org.broadinstitute.sting.queue.extensions.picard._
import net.sf.samtools.{SAMFileReader, SAMReadGroupRecord}
import net.sf.samtools.SAMFileHeader.SortOrder
class DataProcessingPipeline extends QScript {
@ -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
/****************************************************************************
@ -180,6 +182,7 @@ class DataProcessingPipeline extends QScript {
var realignedBams: List[File] = List()
var index = 1
for (bam <- bams) {
val readSortedBam = swapExt(bam, ".bam", "." + index + ".sorted.bam" )
val saiFile1 = swapExt(bam, ".bam", "." + index + ".1.sai")
val saiFile2 = swapExt(bam, ".bam", "." + index + ".2.sai")
val realignedSamFile = swapExt(bam, ".bam", "." + index + ".realigned.sam")
@ -190,11 +193,12 @@ class DataProcessingPipeline extends QScript {
bwa_sam_se(bam, saiFile1, realignedSamFile))
}
else {
add(bwa_aln_pe(bam, saiFile1, 1),
bwa_aln_pe(bam, saiFile2, 2),
bwa_sam_pe(bam, saiFile1, saiFile2, realignedSamFile))
add(sortSam(bam, readSortedBam, SortOrder.queryname),
bwa_aln_pe(readSortedBam, saiFile1, 1),
bwa_aln_pe(readSortedBam, saiFile2, 2),
bwa_sam_pe(readSortedBam, saiFile1, saiFile2, realignedSamFile))
}
add(sortSam(realignedSamFile, realignedBamFile))
add(sortSam(realignedSamFile, realignedBamFile, SortOrder.coordinate))
addReadGroups(realignedBamFile, rgRealignedBamFile, new SAMFileReader(bam))
realignedBams :+= rgRealignedBamFile
index = index + 1
@ -385,9 +389,10 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".joinBams"
}
case class sortSam (inSam: File, outBam: File) extends SortSam {
case class sortSam (inSam: File, outBam: File, sortOrderP: SortOrder) extends SortSam {
this.input = List(inSam)
this.output = outBam
this.sortOrder = sortOrderP
this.memoryLimit = 4
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".sortSam"
@ -430,7 +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"
}
@ -438,7 +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"
}