Commit ceaa8fd0 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Handle RNA seq files, sam filter only takes the primary alignment

parent b4a13e74
......@@ -69,7 +69,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
// sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
val samFilterUnmapped = new SambambaView(qscript)
samFilterUnmapped.input = bamfile
samFilterUnmapped.filter = Some("unmapped or mate_is_unmapped")
samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment)")
samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
samFilterUnmapped.isIntermediate = false
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