Commit 90815888 authored by Sander Bollen's avatar Sander Bollen

last bits

parent 992d265a
......@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by Sander Bollen on 23-11-16.
......@@ -44,6 +44,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Output
var cumulativeCoverageProportionsFile = _cumulativeCoverageProportionsFile
@Input(required = false)
var calculateCoverageOverGenes: Option[File] = config("calculate_coverage_over_genes", namespace = "depth_of_coverage", default = None)
var countType: Option[String] = config("count_type", namespace = "depth_of_coverage", default = None)
......@@ -126,3 +127,13 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
conditional(printBinEndpointsAndExit, "--printBinEndPointsAndExit")
}
}
object DepthOfCoverage {
def apply(root: Configurable, bamFile: List[File], outFile: File, targets: List[File]): DepthOfCoverage = {
val dp = new DepthOfCoverage(root)
dp.input_file = bamFile
dp.intervals = targets
dp.out = outFile
dp
}
}
......@@ -13,7 +13,7 @@ class XhmmPca(val root: Configurable) extends Xhmm {
@Input
var inputMatrix: File = _
@Output
@Output(required = true)
var pcaFile: File = _
def cmdLine = {
......
......@@ -35,7 +35,9 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
}
def biopetScript() = {
val depths = inputBams.map(keyValuePair => depthOfCoverage(keyValuePair._2)).toList
val depths = inputBams.map { keyValuePair =>
DepthOfCoverage(this, List(keyValuePair._2), swapExt(xhmmDir, ".bam", ".dcov"), List(targets))
}.toList
addAll(depths)
// merging of gatk depths files
......
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