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

Change val name

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