Commit 3eb42a6b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed some of the tags for picard summaries

parent c82a2851
......@@ -72,16 +72,15 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
case _ if p == Programs.CollectAlignmentSummaryMetrics.toString =>
Picard.getMetrics(new File(outputName + ".alignment_summary_metrics")).getOrElse(Map())
case _ if p == Programs.CollectInsertSizeMetrics.toString =>
Map()
Picard.getMetrics(new File(outputName + ".insert_size_metrics")).getOrElse(Map())
Map(
"metrics" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics")).getOrElse(Map()),
"histogram" -> Picard.getMetrics(new File(outputName + ".insert_size_metrics"), "HISTOGRAM").getOrElse(Map())
)
case _ if p == Programs.QualityScoreDistribution.toString =>
Map()
Picard.getMetrics(new File(outputName + ".quality_distribution_metrics")).getOrElse(Map())
Picard.getMetrics(new File(outputName + ".quality_distribution_metrics"), "HISTOGRAM").getOrElse(Map())
case _ if p == Programs.MeanQualityByCycle.toString =>
Map()
Picard.getMetrics(new File(outputName + ".quality_by_cycle_metrics")).getOrElse(Map())
Picard.getMetrics(new File(outputName + ".quality_by_cycle_metrics"), "HISTOGRAM").getOrElse(Map())
case _ if p == Programs.CollectBaseDistributionByCycle.toString =>
Map()
Picard.getMetrics(new File(outputName + ".base_distribution_by_cycle_metrics")).getOrElse(Map())
case _ => Map()
}
......
Supports Markdown
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