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Don't set base qualities if fastQ is provided 

* Pacbio Processing pipeline now works with the new fastQ files outputted by the Pacbio instrument
This commit is contained in:
Mauricio Carneiro 2012-01-23 17:56:27 -05:00
parent b6c816fe12
commit 2bb9525e7f
1 changed files with 7 additions and 4 deletions
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9
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -1,7 +1,6 @@
package org.broadinstitute.sting.queue.qscripts package org.broadinstitute.sting.queue.qscripts
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.util.QScriptUtils import org.broadinstitute.sting.queue.util.QScriptUtils
import net.sf.samtools.SAMFileHeader.SortOrder import net.sf.samtools.SAMFileHeader.SortOrder
import org.broadinstitute.sting.utils.exceptions.UserException import org.broadinstitute.sting.utils.exceptions.UserException
@ -60,12 +59,15 @@ class PacbioProcessingPipeline extends QScript {
for (file: File <- fileList) { for (file: File <- fileList) {
var USE_BWA: Boolean = false var USE_BWA: Boolean = false
var resetQuals: Boolean = true
if (file.endsWith(".fasta") || file.endsWith(".fq")) { if (file.endsWith(".fasta") || file.endsWith(".fq")) {
if (bwaPath == null) { if (bwaPath == null) {
throw new UserException("You provided a fasta/fastq file but didn't provide the path for BWA"); throw new UserException("You provided a fasta/fastq file but didn't provide the path for BWA");
} }
USE_BWA = true USE_BWA = true
if (file.endsWith(".fq"))
resetQuals = false
} }
// FASTA -> BAM steps // FASTA -> BAM steps
@ -99,7 +101,7 @@ class PacbioProcessingPipeline extends QScript {
add(cov(bam, recalFile1), add(cov(bam, recalFile1),
recal(bam, recalFile1, recalBam), recal(bam, recalFile1, recalBam),
cov(recalBam, recalFile2), cov(recalBam, recalFile2, resetQuals),
analyzeCovariates(recalFile1, path1), analyzeCovariates(recalFile1, path1),
analyzeCovariates(recalFile2, path2)) analyzeCovariates(recalFile2, path2))
} }
@ -158,7 +160,8 @@ class PacbioProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".rg" this.jobName = queueLogDir + outBam + ".rg"
} }
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs { case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends CountCovariates with CommandLineGATKArgs {
if (resetQuals)
this.DBQ = dbq this.DBQ = dbq
this.knownSites :+= dbSNP this.knownSites :+= dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")