Commit ff81ebd3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added sampe

parent 1f867d68
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 BwaSampe (val root: Configurable) extends Bwa {
@Input(doc = "Fastq file R1", required = true)
var fastqR1: File = _
@Input(doc = "Fastq file R2", required = true)
var fastqR2: File = _
@Input(doc = "Sai file R1", required = true)
var saiR1: File = _
@Input(doc = "Sai file R2", required = true)
var saiR2: 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 a: Option[Int] = config("a")
var o: Option[Int] = config("o")
var n: Option[Int] = config("n")
var N: Option[Int] = config("N")
var c: Option[Float] = config("c")
var P: Boolean = config("P", default = false)
var s: Boolean = config("s", default = false)
var A: Boolean = config("A", default = false)
var r: String = _
def cmdLine = required(executable) +
required("samse") +
optional("-n", n) +
optional("-f", output) +
optional("-r", r) +
optional("-c", c) +
conditional(P, "-P") +
conditional(s, "-s") +
conditional(A, "-A") +
required(reference) +
required(saiR1) +
required(saiR2) +
required(fastqR1) +
required(fastqR2)
}
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