Commit 52e6c553 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix reference

parent 4a368a8b
......@@ -21,14 +21,14 @@ import htsjdk.variant.variantcontext.VariantContext
import htsjdk.variant.vcf.VCFFileReader
import java.io.File
import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.{ ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion, BiopetJavaCommandLineFunction, ToolCommand }
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import nl.lumc.sasc.biopet.utils.VcfUtils._
import scala.collection.mutable.ListBuffer
class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion {
class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
javaMainClass = getClass.getName
@Input(doc = "Input vcf file", required = false)
......@@ -38,7 +38,7 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion {
var bamFile: File = _
@Input(doc = "reference", required = false)
var reference: File = config("reference")
var reference: File = _
@Output(doc = "Output fasta, variants only", required = false)
var outputVariants: File = _
......@@ -57,6 +57,11 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion {
override val defaultCoreMemory = 4.0
override def beforeGraph: Unit = {
super.beforeGraph
reference = referenceFasta()
}
override def commandLine = super.commandLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
......
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