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Commit 85f91910 authored by bow's avatar bow
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Add CollectRnaSeqMetrics histogram to summary file

parent 657d8684
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...@@ -85,7 +85,9 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza ...@@ -85,7 +85,9 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
"output_chart" -> chartOutput "output_chart" -> chartOutput
).collect { case (key, Some(value)) => key -> value } ).collect { case (key, Some(value)) => key -> value }
def summaryStats = Picard.getMetrics(output).getOrElse(Map()) def summaryStats = Map(
"metrics" -> Picard.getMetrics(output).getOrElse(Map()),
"histogram" -> Picard.getHistogram(output).getOrElse(Map()))
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("INPUT=", input, spaceSeparated = false) + required("INPUT=", input, spaceSeparated = false) +
......
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