Commit 6719e995 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change val name

parent 5ff11a3c
......@@ -38,13 +38,13 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
case (id, file) =>
val bamFile = if (sortOnId) {
val samtoolsSort = new SortSam(this)
samtoolsSort.input = file
samtoolsSort.output = swapExt(outputDir, file, ".bam", ".idsorted.bam")
samtoolsSort.sortOrder = "queryname"
samtoolsSort.isIntermediate = true
val sortSam = new SortSam(this)
sortSam.input = file
sortSam.output = swapExt(outputDir, file, ".bam", ".idsorted.bam")
sortSam.sortOrder = "queryname"
sortSam.isIntermediate = true
} else file
val job = new HtseqCount(this)
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