Commit 3dac3272 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added wgs histogram

parent 7d824f77
......@@ -30,7 +30,7 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
var minBaseQ: Option[Int] = config("minimum_base_quality")
@Argument(doc = "COVERAGE_CAP", required = false)
var covCap: Option[Int] = config("coverage_cap")
var covCap: Option[Int] = config("coverage_cap", default = 401)
@Argument(doc = "STOP_AFTER", required = false)
var stopAfter: Option[Long] = config("stop_after")
......@@ -57,5 +57,8 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
def summaryFiles: Map[String, File] = Map()
/** Returns stats for summary */
def summaryStats = Picard.getMetrics(output).getOrElse(Map())
def summaryStats = Map(
"metrics" -> Picard.getMetrics(output),
"histogram" -> Picard.getHistogram(output)
)
}
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