Commit 700bfa35 authored by bow's avatar bow
Browse files

Precompile regex for splitting read IDs

parent 20dab674
...@@ -90,9 +90,12 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction { ...@@ -90,9 +90,12 @@ class FastqSync(val root: Configurable) extends BiopetJavaCommandLineFunction {
object FastqSync extends ToolCommand { object FastqSync extends ToolCommand {
/** Regex for capturing read ID ~ taking into account its read pair mark (if present) */
private val idRegex = "[_/][12]\\s??|\\s".r
/** Implicit class to allow for lazy retrieval of FastqRecord ID without any read pair mark */ /** Implicit class to allow for lazy retrieval of FastqRecord ID without any read pair mark */
private implicit class FastqPair(fq: FastqRecord) { private implicit class FastqPair(fq: FastqRecord) {
lazy val fragId = fq.getReadHeader.split("[_/][12]\\s??|\\s")(0) lazy val fragId = idRegex.split(fq.getReadHeader)(0)
} }
/** /**
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