Commit 183c3f33 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change file extension for better igv support

parent 9bdd717f
......@@ -46,14 +46,14 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
val igvCount = new IGVToolsCount(this)
igvCount.input = bamFile
igvCount.genomeChromSizes = bs.chromSizesFile
igvCount.wig = Some(swapExt(outputDir, bamFile, ".bam", ".wig"))
igvCount.tdf = Some(swapExt(outputDir, bamFile, ".bam", ".tdf"))
igvCount.wig = Some(new File(outputDir, bamFile.getName + ".wig"))
igvCount.tdf = Some(new File(outputDir, bamFile.getName + ".tdf"))
val wigToBigWig = new WigToBigWig(this)
wigToBigWig.inputWigFile = igvCount.wig.get
wigToBigWig.inputChromSizesFile = bs.chromSizesFile
wigToBigWig.outputBigWig = swapExt(outputDir, bamFile, ".bam", ".bw")
wigToBigWig.outputBigWig = new File(outputDir, bamFile.getName + ".bw")
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