Commit 87437ea0 authored by Sander Bollen's avatar Sander Bollen

sync z beds

parent ea2f420c
......@@ -4,7 +4,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, PedigreeQscript, PipelineCommand, Reference }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsSort
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsIntersect, BedtoolsSort }
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Gzip, Ln, Tabix }
import nl.lumc.sasc.biopet.extensions.gatk.DepthOfCoverage
import nl.lumc.sasc.biopet.extensions.wisecondor.{ WisecondorCount, WisecondorGcCorrect, WisecondorNewRef, WisecondorZscore }
......@@ -91,7 +91,30 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
sample -> createXhmmZscore(sample, jobsAndRefFile._2)
}
addAll(wisecondorZJobs.values.toList ::: (xhmmZJobs.values.map(_._1).toList ::: wisecondorRefJobs.values.map(_._1).toList ::: xhmmRefJobs.values.map(_._1).toList).flatten)
val wisecondorSyncJobs = wisecondorZJobs map {
case (sample, job) =>
val intersect = new BedtoolsIntersect(this)
intersect.input = job.output
intersect.intersectFile = xhmmZJobs(sample)._2
intersect.output = new File(sample.sampleDir, s"${sample.sampleId}.wisecondor.sync.z.bed")
sample -> intersect
}
val xhmmSyncJobs = xhmmZJobs map {
case (sample, jobsAndFile) =>
val intersect = new BedtoolsIntersect(this)
intersect.input = jobsAndFile._2
intersect.intersectFile = wisecondorZJobs(sample).output
intersect.output = new File(sample.sampleDir, s"${sample.sampleId}.xhmm.sync.z.bed")
sample -> intersect
}
addAll(xhmmRefJobs.values.flatMap(_._1))
addAll(wisecondorRefJobs.values.flatMap(_._1))
addAll(xhmmZJobs.values.flatMap(_._1))
addAll(wisecondorZJobs.values)
addAll(wisecondorSyncJobs.values)
addAll(xhmmSyncJobs.values)
}
/**
......
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