From b2da50cbe4ff0004fdc5338a0df879e061dd0f9d Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Thu, 5 Feb 2015 15:44:11 +0100
Subject: [PATCH] Making the output files Option[File], and use Some() to
verify whether it was set or not
---
.../extensions/igvtools/IGVToolsCount.scala | 20 +++++++++----------
1 file changed, 10 insertions(+), 10 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 2f6275176..4c5f1f255 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
@@ -20,10 +20,10 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var genomeChromSizes: File = _
@Output
- protected var tdf: File = _
+ protected var tdf: Option[File] = _
@Output
- protected var wig: File = _
+ protected var wig: Option[File] = _
var maxZoom: Option[Int] = config("maxZoom")
var windowSize: Option[Int] = config("windowSize")
@@ -46,8 +46,8 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
super.afterGraph
if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
- this.tdf = new File(input.getAbsolutePath + ".tdf")
- this.wig = new File(input.getAbsolutePath.stripSuffix(".bam") + ".wig")
+ this.tdf = Some(new File(input.getAbsolutePath + ".tdf"))
+ this.wig = Some(new File(input.getAbsolutePath.stripSuffix(".bam") + ".wig"))
}
def cmdLine = {
@@ -72,14 +72,14 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
/**
* This part should never fail, these values are set within this wrapper
- *
+ *
*/
private def outputArg: String = {
- (tdf.isInstanceOf[File], wig.isInstanceOf[File]) match {
- case (false, false) => throw new IllegalArgumentException("Either TDF or WIG should be supplied");
- case (true, false) => tdf.getAbsolutePath;
- case (false, true) => wig.getAbsolutePath;
- case (true, true) => tdf.getAbsolutePath + "," + wig.getAbsolutePath;
+ (tdf, wig) match {
+ case (None, None) => throw new IllegalArgumentException("Either TDF or WIG should be supplied");
+ case (Some(a), None) => a.getAbsolutePath;
+ case (None, Some(b)) => b.getAbsolutePath;
+ case (Some(a), Some(b)) => a.getAbsolutePath + "," + b.getAbsolutePath;
}
}
}
--
GitLab