Commit e929b76a authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Make setting the tdf/wig less restrictive and no default names anymore

parent b2da50cb
package nl.lumc.sasc.biopet.extensions.igvtools
import java.nio.file.InvalidPathException
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
import{ FileNotFoundException, File }
......@@ -20,10 +22,10 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var genomeChromSizes: File = _
protected var tdf: Option[File] = _
var tdf: Option[File] = _
protected var wig: Option[File] = _
var wig: Option[File] = _
var maxZoom: Option[Int] = config("maxZoom")
var windowSize: Option[Int] = config("windowSize")
......@@ -46,8 +48,8 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
this.tdf = Some(new File(input.getAbsolutePath + ".tdf"))
this.wig = Some(new File(input.getAbsolutePath.stripSuffix(".bam") + ".wig"))
if (!wig.isEmpty && !wig.get.getAbsolutePath.endsWith(".wig")) throw new IllegalArgumentException("Wiggle file should have a .wig file-extension")
if (!tdf.isEmpty && !tdf.get.getAbsolutePath.endsWith(".tdf")) throw new IllegalArgumentException("TDF file should have a .tdf file-extension")
def cmdLine = {
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment