120 lines
4.4 KiB
Scala
120 lines
4.4 KiB
Scala
package oneoffs.fromer
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.util.VCF_BAM_utilities
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class PhaseSamples extends QScript {
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qscript =>
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@Input(doc = "bam input, as .bam or as a list of files", shortName = "I", required = true)
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var bams: File = _
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@Input(doc = "master VCF calls", shortName = "C", required = true)
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var masterCalls: File = _
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@Argument(doc = "gatk jar file", shortName = "J", required = true)
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var gatkJarFile: File = _
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@Argument(shortName = "R", doc = "ref", required = true)
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var referenceFile: File = _
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@Argument(fullName = "prefix", doc = "Prefix argument", required = false)
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var prefix: String = ""
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@Argument(shortName = "L", doc = "Intervals", required = false)
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var intervals: String = null
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@Input(doc = "level of parallelism for BAM phaser. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
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var scatterCount = 0
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@Input(doc = "Samples to phase together. By default is set to 1 [one job per sample].", shortName = "samplesPerJob", required = false)
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var samplesPerJob = 1
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@Output(doc = "Phased file to output", shortName = "o", required = true)
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var outputPhased: File = _
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trait CommandLineGATKArgs extends CommandLineGATK {
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if (qscript.intervals != null) {
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this.intervalsString = List(qscript.intervals)
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}
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this.jarFile = qscript.gatkJarFile
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this.reference_sequence = qscript.referenceFile
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this.memoryLimit = 3
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this.logging_level = "INFO"
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}
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// A target has a list of samples and bam files to use for phasing
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class Target(val name: String, val samples: List[String], val bams: List[File]) {
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var prefix: String = outputPhased.getParent()
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if (prefix == null)
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prefix = ""
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else
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prefix = prefix + "/"
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def phasedVCFFile = new File(prefix + name + "." + outputPhased.getName())
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override def toString(): String = String.format("[Target %s [%s] with samples %s against bams %s]", name, phasedVCFFile, samples, bams)
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}
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def script = {
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if (qscript.scatterCount > 0) throw new RuntimeException("scatter/gather currently not implemented")
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val samples: List[String] = VCF_BAM_utilities.getSamplesFromVCF(masterCalls)
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Console.out.printf("Samples are %s%n", samples)
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val targets: List[Target] = bamsToTargets(samples, bams)
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for (target <- targets) {
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Console.out.printf("Target is %s%n", target)
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add(new PhaseSamples(target))
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}
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add(new CombineVariants(targets.map(_.phasedVCFFile)))
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add(new PhasingByACeval())
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}
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def bamsToTargets(samples: List[String], bamsIn: File): List[Target] = {
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val bams: List[File] = VCF_BAM_utilities.parseBAMsInput(bamsIn)
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val sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = VCF_BAM_utilities.getMapOfBAMsForSample(bams)
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def buildTargets(samples: List[String], count: Int): List[Target] = (samples splitAt samplesPerJob) match {
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case (Nil, y) =>
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return Nil
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case (subsamples, remaining) =>
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return new Target("group" + count, subsamples, VCF_BAM_utilities.findBAMsForSamples(subsamples, sampleToBams)) ::
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buildTargets(remaining, count + 1)
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}
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return buildTargets(samples, 0)
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}
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class PhaseSamples(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ReadBackedPhasing with CommandLineGATKArgs {
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this.rodBind :+= RodBind("variant", "VCF", qscript.masterCalls)
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this.out = t.phasedVCFFile
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this.input_file = t.bams
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this.sampleToPhase = t.samples
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}
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class CombineVariants(vcfsToCombine: List[File]) extends org.broadinstitute.sting.queue.extensions.gatk.CombineVariants with CommandLineGATKArgs {
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for (vcf <- vcfsToCombine) {
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this.rodBind :+= RodBind(vcf.getName, "VCF", vcf)
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}
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// add the master call:
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this.rodBind :+= RodBind("master", "VCF", masterCalls)
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this.variantMergeOptions = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.MASTER
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this.out = outputPhased
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}
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class PhasingByACeval() extends org.broadinstitute.sting.queue.extensions.gatk.PhasingEval with CommandLineGATKArgs {
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this.analysis = org.broadinstitute.sting.oneoffprojects.walkers.phasing.PhasingEval.Analysis.PHASING_BY_AC
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this.rodBind :+= RodBind(outputPhased.getName, "VCF", outputPhased)
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this.out = new File("phasing_by_ac." + outputPhased + ".txt")
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}
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} |