Commit 39772398 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

enableRCtrimming is used to enable trimming of Reverse Complement versions of adapters

parent 9e3d9653
......@@ -35,6 +35,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
/** Allow reporting of all found (potentially adapter) sequences in the FastQC */
var sensitiveAdapterSearch: Boolean = config("sensitiveAdapterSearch", default = false)
var enableRCtrimming: Boolean = config("enableRCtrimming", default=false)
/** Class for storing a single FastQC module result */
protected case class FastQCModule(name: String, status: String, lines: Seq[String])
......@@ -188,9 +189,9 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
val fromKnownList: Set[AdapterSequence] = (adapterSet ++ contaminantSet)
.filter(x => foundAdapterNames.exists(_.startsWith(x.name)))
val fromKnownListRC: Set[AdapterSequence] = fromKnownList.map {
val fromKnownListRC: Set[AdapterSequence] = if(enableRCtrimming) fromKnownList.map {
x => AdapterSequence(x.name + "_RC", reverseComplement(x.seq))
}
} else Set.empty
// list all sequences found by FastQC
val fastQCFoundSequences: Seq[AdapterSequence] = if (sensitiveAdapterSearch) {
......
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