Commit f6796a24 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix Cutadapt statistics to store Long values. Tests hit the Int.max

parent a548cfde
......@@ -182,7 +182,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
val basePairsProcessed = """Total basepairs processed: *([,\d]+) bp""".r
val basePairsWritten = """Total written \(filtered\): *([,\d]+) bp .*""".r
val stats: mutable.Map[String, Int] = mutable.Map(
val stats: mutable.Map[String, Long] = mutable.Map(
"processed" -> 0,
"withadapters" -> 0,
"passingfilters" -> 0,
......@@ -192,21 +192,21 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
"bpoutput" -> 0,
"toomanyn" -> 0
)
val adapter_stats: mutable.Map[String, Int] = mutable.Map()
val adapter_stats: mutable.Map[String, Long] = mutable.Map()
if (statsOutput.exists) {
val statsFile = Source.fromFile(statsOutput)
for (line <- statsFile.getLines()) {
line match {
case processedReads(m) => stats("processed") = m.replaceAll(",", "").toInt
case withAdapters(m) => stats("withadapters") = m.replaceAll(",", "").toInt
case readsPassingFilters(m) => stats("passingfilters") = m.replaceAll(",", "").toInt
case tooShortR(m) => stats("tooshort") = m.replaceAll(",", "").toInt
case tooLongR(m) => stats("toolong") = m.replaceAll(",", "").toInt
case tooManyN(m) => stats("toomanyn") = m.replaceAll(",", "").toInt
case basePairsProcessed(m) => stats("bpinput") = m.replaceAll(",", "").toInt
case basePairsWritten(m) => stats("bpoutput") = m.replaceAll(",", "").toInt
case adapterR(adapter, count) => adapter_stats += (adapter -> count.toInt)
case processedReads(m) => stats("processed") = m.replaceAll(",", "").toLong
case withAdapters(m) => stats("withadapters") = m.replaceAll(",", "").toLong
case readsPassingFilters(m) => stats("passingfilters") = m.replaceAll(",", "").toLong
case tooShortR(m) => stats("tooshort") = m.replaceAll(",", "").toLong
case tooLongR(m) => stats("toolong") = m.replaceAll(",", "").toLong
case tooManyN(m) => stats("toomanyn") = m.replaceAll(",", "").toLong
case basePairsProcessed(m) => stats("bpinput") = m.replaceAll(",", "").toLong
case basePairsWritten(m) => stats("bpoutput") = m.replaceAll(",", "").toLong
case adapterR(adapter, count) => adapter_stats += (adapter -> count.toLong)
case _ =>
}
}
......
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