From ca0d9e9369cf5177afde9fb82f674797f65a3913 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Feb 2015 11:37:24 +0100
Subject: [PATCH] Added a apply function
---
.../sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala | 13 ++++++++++++-
1 file changed, 12 insertions(+), 1 deletion(-)
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index 9af1eee60..4579851bd 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -1,5 +1,7 @@
package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+import java.io.File
+
import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.WigToBigWig
@@ -41,4 +43,13 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
}
}
-object Bam2Wig extends PipelineCommand
\ No newline at end of file
+object Bam2Wig extends PipelineCommand {
+ def apply(root: Configurable, bamFile: File): Bam2Wig = {
+ val bamToBigWig = new Bam2Wig(root)
+ bamToBigWig.outputDir = bamFile.getParent
+ bamToBigWig.bamFile = bamFile
+ bamToBigWig.init()
+ bamToBigWig.biopetScript()
+ bamToBigWig
+ }
+}
\ No newline at end of file
--
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