From e929b76a8c4b7b6290b8d9a38e475a06fdabfc15 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Thu, 5 Feb 2015 17:29:33 +0100
Subject: [PATCH] Make setting the tdf/wig less restrictive and no default
names anymore
---
.../biopet/extensions/igvtools/IGVToolsCount.scala | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
index 4c5f1f255..803761683 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
@@ -1,6 +1,8 @@
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 java.io.{ FileNotFoundException, File }
@@ -20,10 +22,10 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var genomeChromSizes: File = _
@Output
- protected var tdf: Option[File] = _
+ var tdf: Option[File] = _
@Output
- 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 {
super.afterGraph
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 = {
--
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