Commit 9461ff47 authored by Peter van 't Hof's avatar Peter van 't Hof

Put scattering back in for baserecalibration

parent f6bfca5d
......@@ -16,17 +16,16 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, Input }
//TODO: check gathering
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with ScatterGatherableFunction */ {
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "BaseRecalibrator"
//TODO: check gathering
//scatterClass = classOf[ContigScatterFunction]
//setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
scatterClass = classOf[ContigScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
/** A database of known polymorphic sites */
@Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites", required = false, exclusiveOf = "", validation = "")
......@@ -38,7 +37,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
/** The output recalibration table file to create */
@Output(fullName = "out", shortName = "o", doc = "The output recalibration table file to create", required = true, exclusiveOf = "", validation = "") //TODO: check gathering
//@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
var out: File = _
/** One or more covariates to be used in the recalibration. Can be specified multiple times */
......
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