Commit cfdfd0b9 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

added bam metrics for filtered file

parent e93bf522
......@@ -124,11 +124,20 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"), sampleId = Some(sampleId))
val bamMetricsFilter = BamMetrics(qscript, bamFileFilter, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId))
bamMetricsFilter.summaryName = "bamMetrics-filter"
addAll(Bam2Wig(qscript, bamFile).functions)
addAll(Bam2Wig(qscript, bamFileFilter).functions)
val samtoolsView = new SamtoolsView(qscript)
samtoolsView.input = bamFile
samtoolsView.output = bamFileFilter
samtoolsView.b = true
samtoolsView.h = true
val buildBamIndex = new BuildBamIndex(qscript)
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