Commit b17079d8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added samtools sort

parent 3482754f
package nl.lumc.sasc.biopet.extensions.samtools
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
/**
* Created by pjvanthof on 22/09/15.
*/
class SamtoolsSort(val root: Configurable) extends Samtools {
@Input(required = true)
var input: File = _
@Output
var output: File = _
val compresion: Option[Int] = config("l")
val outputFormat: Option[String] = config("O")
val sortByName: Boolean = config("sort_by_name", default = false)
val prefix: String = config("prefix", default = new File(qSettings.tempDirectory, output.getAbsolutePath))
def cmdLine = optional("-m", (coreMemeory + "G")) +
optional("-@", threads) +
optional("-O", outputFormat) +
conditional(sortByName, "-n") +
(if (outputAsStsout) "" else required("-o", output)) +
(if (inputAsStdin) "" else required(input))
}
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