Commit 0929d425 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added bam index file as output file

parent d107727c
......@@ -8,8 +8,12 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Output
class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
@Output
protected var bamIndex: File = _
if (config.contains("scattercount")) scatterCount = config("scattercount")
}
......@@ -19,6 +23,7 @@ object IndelRealigner {
ir.input_file :+= input
ir.targetIntervals = targetIntervals
ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
ir.bamIndex = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bai")
ir
}
}
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