Commit 83e4d44a authored by bow's avatar bow
Browse files

Use correct types for JSON output in cutadapt summary

parent fb8373ab
......@@ -41,7 +41,7 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
val adapterR = """Adapter '([C|T|A|G]*)'.*trimmed (\d*) times.""".r
val stats: mutable.Map[String, Int] = mutable.Map("trimmed" -> 0, "tooshort" -> 0, "toolong" -> 0)
val adapter_stats: mutable.Map[String, (String, Int)] = mutable.Map()
val adapter_stats: mutable.Map[String, List[Any]] = mutable.Map()
if (stats_output.exists) for (line <- Source.fromFile(stats_output).getLines) {
line match {
......@@ -53,7 +53,7 @@ class Cutadapt(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Cutada
case None => "unknown"
case Some(a) => a.name
}
adapter_stats += (adapter -> (adapterName, count.toInt))
adapter_stats += (adapterName -> List(adapter, count.toInt))
case _ =>
}
}
......
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