Merge pull request #8 from biopet/fix-BIOPET-513

Harmonize flagstat keys

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -150,6 +150,10 @@ class BamMetrics(val root: Configurable) extends QScript
     }
 
     // Create stats and coverage plot for each bed/interval file
+    val allIntervalNames = (roiIntervals ++ ampIntervals).map(_.bed.getName)
+    if (allIntervalNames.size != allIntervalNames.toSet.size) {
+      logger.warn("There are multiple region files with the same name. Metric values might get overwritten")
+    }
     for (intervals <- roiIntervals ++ ampIntervals) {
       val targetName = intervals.bed.getName.stripSuffix(".bed")
       val targetDir = new File(outputDir, targetName)
@@ -158,14 +162,14 @@ class BamMetrics(val root: Configurable) extends QScript
         output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.sam"),
         minOverlap = config("strict_intersect_overlap", default = 1.0))
       val biopetFlagstatStrict = BiopetFlagstat(this, biStrict.output, targetDir)
-      addSummarizable(biopetFlagstatStrict, targetName + "_biopet_flagstat_strict")
+      addSummarizable(biopetFlagstatStrict, targetName + "_flagstats_strict")
       add(new BiopetFifoPipe(this, List(biStrict, biopetFlagstatStrict)))
 
       val biLoose = BedtoolsIntersect(this, inputBam, intervals.bed,
         output = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.sam"),
         minOverlap = config("loose_intersect_overlap", default = 0.01))
       val biopetFlagstatLoose = BiopetFlagstat(this, biLoose.output, targetDir)
-      addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
+      addSummarizable(biopetFlagstatLoose, targetName + "_flagstats_loose")
       add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
 
       val sortedBed = BamMetrics.sortedbedCache.getOrElse(intervals.bed, {