Commit 63090796 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added squish bed extension

parent 9bbaa813
......@@ -2,12 +2,31 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.{ToolCommandFuntion, ToolCommand}
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.broadinstitute.gatk.utils.commandline.{Output, Input}
/**
* Created by pjvanthof on 22/08/15.
*/
class SquishBed(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = getClass.getName
@Input(doc = "Input Bed file", required = true)
var input: File = _
@Output(doc = "Output interval list", required = true)
var output: File = _
var strandSensitive: Boolean = config("strandSensitive", default = false)
override def commandLine = super.commandLine +
required("-I", input) +
required("-o", output) +
conditional(strandSensitive, "-s")
}
object SquishBed extends ToolCommand {
case class Args(input: File = null,
......
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