Commit 1f867d68 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added samse

parent 7bea64ef
package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 1/16/15.
*/
class BwaSamse(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file", required = true)
var fastq: File = _
@Input(doc = "Sai file", required = true)
var sai: File = _
@Input(doc = "The reference file for the bam files.", required = true)
var reference: File = config("reference", required = true)
@Output(doc = "Output file SAM", required = false)
var output: File = _
var n: Option[Int] = config("n")
var r: String = _
def cmdLine = required(executable) +
required("samse") +
optional("-n", n) +
optional("-f", output) +
optional("-r", r) +
required(reference) +
required(sai) +
required(fastq)
}
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