Commit 2d950663 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix sample bamMetrics

parent 334a0969
...@@ -186,8 +186,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit ...@@ -186,8 +186,13 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
object BamMetrics extends PipelineCommand { object BamMetrics extends PipelineCommand {
/** Make default implementation of BamMetrics and runs script already */ /** Make default implementation of BamMetrics and runs script already */
def apply(root: Configurable, bamFile: File, outputDir: File): BamMetrics = { def apply(root: Configurable,
bamFile: File, outputDir: File,
sampleId: Option[String] = None,
libId: Option[String] = None): BamMetrics = {
val bamMetrics = new BamMetrics(root) val bamMetrics = new BamMetrics(root)
bamMetrics.sampleId = sampleId
bamMetrics.libId = libId
bamMetrics.inputBam = bamFile bamMetrics.inputBam = bamFile
bamMetrics.outputDir = outputDir bamMetrics.outputDir = outputDir
......
...@@ -107,7 +107,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with ...@@ -107,7 +107,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
add(merge) add(merge)
} }
val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics")) val bamMetrics = BamMetrics(qscript, bamFile, new File(sampleDir, "metrics"), sampleId = Some(sampleId))
addAll(bamMetrics.functions) addAll(bamMetrics.functions)
addSummaryQScript(bamMetrics) addSummaryQScript(bamMetrics)
addAll(Bam2Wig(qscript, bamFile).functions) addAll(Bam2Wig(qscript, bamFile).functions)
......
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