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biopet.biopet
Commit e6ed0297 authored by Sander Bollen's avatar Sander Bollen
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harmonize summary keys for flagstats

parent 31be1177
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Showing with 2 additions and 2 deletions
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @ e6ed0297
......@@ -158,14 +158,14 @@ 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, {
......
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