Commit 1df0636d authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

add BuildBamIndex to biopet

parent 95b665ed
package nl.lumc.sasc.biopet.extensions.picard
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
/**
* Created by sajvanderzeeuw on 6-10-15.
*/
class BuildBamIndex (val root: Configurable) extends Picard {
javaMainClass = new picard.sam.BuildBamIndex().getClass.getName
@Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: File = _
@Output(doc = "The output file to bam file to", required = true)
var output: File = _
override def cmdLine = super.cmdLine +
required("INPUT=", input, spaceSeparated = false) +
required("OUTPUT=", output, spaceSeparated = false)
}
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