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now with the new 'consensus model' parameter to the cleaner. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6064 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
droazen 2011-06-22 22:55:42 +00:00
parent c956e154a0
commit c8124496d0
1 changed files with 16 additions and 11 deletions
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27
scala/qscript/core/DataProcessingPipeline.scala
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@ -9,6 +9,7 @@ import net.sf.samtools.{SAMFileReader,SAMReadGroupRecord}
import scala.io.Source._
import collection.JavaConversions._
import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
class DataProcessingPipeline extends QScript {
@ -77,11 +78,8 @@ class DataProcessingPipeline extends QScript {
@Input(doc="an intervals file to be used by GATK - output bams at intervals only", fullName="gatk_interval_file", shortName="intervals", required=false)
var intervals: File = _
@Input(doc="Perform cleaning on knowns only", fullName="knowns_only", shortName="knowns", required=false)
var knownsOnly: Boolean = false
@Input(doc="Perform cleaning using Smith Waterman", fullName="use_smith_waterman", shortName="sw", required=false)
var useSW: Boolean = false
@Input(doc="Cleaning model: KNOWNS_ONLY, USE_READS or USE_SW", fullName="clean_model", shortName="cm", required=false)
var cleaningModel: String = "USE_READS"
@Input(doc="Decompose input BAM file and fully realign it using BWA and assume Single Ended reads", fullName="use_bwa_single_ended", shortName="bwase", required=false)
var useBWAse: Boolean = false
@ -97,6 +95,14 @@ class DataProcessingPipeline extends QScript {
val queueLogDir: String = ".qlog/" // Gracefully hide Queue's output
var nContigs: Int = 0 // Use the number of contigs for scatter gathering jobs
var cleanModelEnum: ConsensusDeterminationModel = ConsensusDeterminationModel.USE_READS
if (cleaningModel == "KNOWNS_ONLY") {
cleanModelEnum = ConsensusDeterminationModel.KNOWNS_ONLY
}
else if (cleaningModel == "USE_SW") {
cleanModelEnum = ConsensusDeterminationModel.USE_SW
}
@ -247,7 +253,7 @@ class DataProcessingPipeline extends QScript {
// If this is a 'knowns only' indel realignment run, do it only once for all samples.
val globalIntervals = new File(outputDir + projectName + ".intervals")
if (knownsOnly)
if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY)
add(target(null, globalIntervals))
// Put each sample through the pipeline
@ -259,7 +265,7 @@ class DataProcessingPipeline extends QScript {
val recalBam = swapExt(bam, ".bam", ".clean.dedup.recal.bam")
// Accessory files
val targetIntervals = if (knownsOnly) {globalIntervals} else {swapExt(bam, ".bam", ".intervals")}
val targetIntervals = if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY) {globalIntervals} else {swapExt(bam, ".bam", ".intervals")}
val metricsFile = swapExt(bam, ".bam", ".metrics")
val preRecalFile = swapExt(bam, ".bam", ".pre_recal.csv")
val postRecalFile = swapExt(bam, ".bam", ".post_recal.csv")
@ -270,7 +276,7 @@ class DataProcessingPipeline extends QScript {
add(validate(bam, preValidateLog))
if (!knownsOnly)
if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
add(target(bam, targetIntervals))
add(clean(bam, targetIntervals, cleanedBam),
@ -306,7 +312,7 @@ class DataProcessingPipeline extends QScript {
}
case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
if (!knownsOnly)
if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
this.input_file :+= inBams
this.out = outIntervals
this.mismatchFraction = 0.0
@ -323,8 +329,7 @@ class DataProcessingPipeline extends QScript {
this.out = outBam
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.useOnlyKnownIndels = knownsOnly
this.doNotUseSW = !useSW
this.consensusDeterminationModel = consensusDeterminationModel
this.compress = 0
this.scatterCount = nContigs
this.analysisName = queueLogDir + outBam + ".clean"