144 lines
5.4 KiB
Scala
144 lines
5.4 KiB
Scala
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.gatk._
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class CleanBamFile extends QScript {
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qscript =>
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@Argument(doc="gatk jar", shortName="gatk")
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var gatkJar: File = _
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@Argument(doc="fix mates jar", shortName="fixMates")
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var fixMatesJar: File = _
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@Input(doc="Script that can merge text files, for example Sting/shell/mergeText.sh.", shortName="MTS")
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var mergeTextScript: String = _
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@Argument(doc="base name for output files", shortName="base")
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var baseName: String = _
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@Input(doc="reference genome", shortName="R")
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var referenceFile: File = _
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@Input(doc="recalibrated bam", shortName="I")
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var recalibratedBam: File = _
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@Argument(doc="read group blacklist conversion script that can convert firehose outputs to a GATK blacklist file.", shortName="RGBLS")
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var readGroupBlackListScript: String = _
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@Argument(doc="read group blacklist", shortName="RGBL", required=false)
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var readGroupBlackList: String = _
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@Argument(doc="intervals", shortName="L", required=false)
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var intervals: File = _
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@Argument(doc="Script that can split the interval file by contig, for example Sting/python/splitIntervalsByContig.py.", shortName="RTCSS")
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var targetCreatorScatterScript: String = _
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@Argument(doc="RealignerTargetCreator scatter count. " +
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"Best if it is either 1 or the number of contigs in the interval list. " +
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"If used the compute farm must also be used.", shortName="RTCSC")
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var targetCreatorScatterCount = 0
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@Argument(doc="Script that can split the intervals evenly, for example Sting/shell/splitIntervals.sh.", shortName="IRSS")
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var indelRealignerScatterScript: String = _
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@Argument(doc="IndelRealigner scatter count.", shortName="IRSC")
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var indelRealignerScatterCount = 0
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@Input(doc="dbsnp file", shortName="D")
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var dbsnpFile: File = _
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trait GATKCommonArgs extends CommandLineGATK {
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this.jarFile = qscript.gatkJar
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this.reference_sequence = qscript.referenceFile
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this.intervals = qscript.intervals
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this.input_file :+= recalibratedBam
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this.cleanupTempDirectories = true
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}
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def baseFile(suffix: String) = new File(baseName + suffix)
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def script = {
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val blacklistConverter = new CommandLineFunction {
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@Output(doc="blacklist file") var blacklistFile: File = _
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def commandLine = readGroupBlackListScript + " " + blacklistFile + " " + readGroupBlackList
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}
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if (readGroupBlackList != null) {
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blacklistConverter.blacklistFile = baseFile(".blacklist.txt")
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add(blacklistConverter)
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}
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// -T RealignerTargetCreator -I <input.bam> -R <reference.genome> <interval.list> <blacklist.file> -o <base.name>.merged.intervals
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val targetCreator = new RealignerTargetCreator with GATKCommonArgs
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targetCreator.memoryLimit = Some(2)
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targetCreator.read_group_black_list :+= blacklistConverter.blacklistFile
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targetCreator.out = baseFile(".merged.intervals")
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targetCreator.scatterCount = targetCreatorScatterCount
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targetCreator.setupScatterFunction = {
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case (scatter: IntervalScatterFunction, _) =>
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scatter.splitIntervalsScript = targetCreatorScatterScript
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}
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targetCreator.setupGatherFunction = {
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case (gather: SimpleTextGatherFunction, _) =>
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gather.mergeTextScript = mergeTextScript
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}
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// -T IndelRealigner -I <input.bam> -R <reference.genome> <blacklist.file> -stats <base.name>.indel.stats
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// -O <base.name>.unfixed.cleaned.bam -maxInRam 200000 -targetIntervals <merged.intervals> -D <dbsnp.file>
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val realigner = new IndelRealigner with GATKCommonArgs
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realigner.memoryLimit = Some(4)
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realigner.read_group_black_list :+= blacklistConverter.blacklistFile
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realigner.statisticsFileForDebugging = baseFile(".indel.stats")
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realigner.maxReadsInRam = Some(200000)
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realigner.targetIntervals = targetCreator.out
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realigner.DBSNP = dbsnpFile
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realigner.scatterCount = indelRealignerScatterCount
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val bamIndex = new BamIndexFunction
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if (realigner.scatterCount > 1) {
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realigner.output = baseFile(".cleaned.bam")
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// While gathering run fix mates.
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realigner.setupScatterFunction = {
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case (scatter: IntervalScatterFunction, _) =>
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scatter.splitIntervalsScript = indelRealignerScatterScript
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}
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realigner.setupGatherFunction = {
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case (gather: PicardBamJarFunction, _) =>
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gather.memoryLimit = Some(4)
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gather.jarFile = fixMatesJar
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// Don't pass this AS=true to fix mates!
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gather.assumeSorted = None
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case (gather: SimpleTextGatherFunction, _) =>
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gather.mergeTextScript = mergeTextScript
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}
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bamIndex.bamFile = realigner.output
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} else {
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realigner.output = baseFile(".unfixed.cleaned.bam")
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// Explicitly run fix mates if the function won't be scattered.
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var fixMates = new PicardBamJarFunction {
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// Declare inputs/outputs for dependency tracking.
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@Input(doc="unfixed bam") var unfixed: File = _
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@Output(doc="fixed bam") var fixed: File = _
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def inputBams = List(unfixed)
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def outputBam = fixed
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}
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fixMates.memoryLimit = Some(4)
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fixMates.jarFile = fixMatesJar
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fixMates.unfixed = realigner.output
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fixMates.fixed = baseFile(".cleaned.bam")
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bamIndex.bamFile = fixMates.fixed
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// Add the fix mates explicitly
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add(fixMates)
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}
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add(targetCreator, realigner, bamIndex)
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}
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}
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