Commit 5d77cf57 authored by Sander Bollen's avatar Sander Bollen

horizontal bed

parent 87437ea0
package nl.lumc.sasc.biopet.extensions.stouffbed
import java.io.File
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
import org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by Sander Bollen on 24-4-17.
*/
abstract class Stouffbed extends BiopetCommandLineFunction with Version {
executable = config("exe", namespace = "stouffbed", default = "stouffbed")
@Input
var inputFiles: List[File] = Nil
def versionCommand = executable + " --version"
def versionRegex = """.+, version (.*)""".r
}
package nl.lumc.sasc.biopet.extensions.stouffbed
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Output
/**
* Created by Sander Bollen on 24-4-17.
*/
class StouffbedHorizontal(val parent: Configurable) extends Stouffbed {
@Output
var output: File = _
def cmdLine: String = {
executable +
required("horizontal") +
repeat("-i", inputs) +
required("-o", output)
}
}
......@@ -7,6 +7,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
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.stouffbed.StouffbedHorizontal
import nl.lumc.sasc.biopet.extensions.wisecondor.{ WisecondorCount, WisecondorGcCorrect, WisecondorNewRef, WisecondorZscore }
import nl.lumc.sasc.biopet.extensions.xhmm.{ XhmmMatrix, XhmmMergeGatkDepths, XhmmNormalize, XhmmPca }
import nl.lumc.sasc.biopet.pipelines.tarmac.scripts.SampleFromMatrix
......@@ -109,12 +110,25 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
sample -> intersect
}
val zScoreMergeJobs = samples map {
case (_, sample) =>
val horizontal = new StouffbedHorizontal(this)
val inputs = List(
wisecondorSyncJobs(sample).output,
xhmmSyncJobs(sample).output
)
horizontal.inputFiles = inputs
horizontal.output = new File(sample.sampleDir, s"${sample.sampleId}.horizontal.bed")
sample -> horizontal
}
addAll(xhmmRefJobs.values.flatMap(_._1))
addAll(wisecondorRefJobs.values.flatMap(_._1))
addAll(xhmmZJobs.values.flatMap(_._1))
addAll(wisecondorZJobs.values)
addAll(wisecondorSyncJobs.values)
addAll(xhmmSyncJobs.values)
addAll(zScoreMergeJobs.values)
}
/**
......
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