Commit 04e8b466 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing BIOPET-496

parent 0b4c76c5
...@@ -118,13 +118,13 @@ object BammetricsReport extends ReportBuilder { ...@@ -118,13 +118,13 @@ object BammetricsReport extends ReportBuilder {
tsvWriter.println("\tMapped\tDuplicates\tUnmapped\tSecondary") tsvWriter.println("\tMapped\tDuplicates\tUnmapped\tSecondary")
def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = { def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
val mapped = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "Mapped"), val mapped = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "Mapped"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val duplicates = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "Duplicates"), val duplicates = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "Duplicates"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val total = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "All"), val total = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "All"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val secondary = new SummaryValue(List("bammetrics", "stats", "biopet_flagstat", "NotPrimaryAlignment"), val secondary = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "NotPrimaryAlignment"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val sb = new StringBuffer() val sb = new StringBuffer()
if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t") if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
......
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