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))
addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics)
val bamMetricsFilter = BamMetrics(qscript, bamFileFilter, new File(sampleDir, "metrics-filter"), sampleId = Some(sampleId))
addAll(bamMetricsFilter.functions)
bamMetricsFilter.summaryName = "bamMetrics-filter"
addSummaryQScript(bamMetricsFilter)
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
add(samtoolsView)
val buildBamIndex = new BuildBamIndex(qscript)
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment