Commit 7b78d005 authored by bow's avatar bow
Browse files

Update access modifiers for WipeReads functions

parent 9cd1b9d7
......@@ -35,7 +35,7 @@ object WipeReads {
type OptionMap = Map[String, Any]
case class RawInterval(chrom: String, start: Int, end: Int, strand: String)
object Strand extends Enumeration {
private object Strand extends Enumeration {
type Strand = Value
val Identical, Opposite, Both = Value
}
......@@ -103,7 +103,7 @@ object WipeReads {
else
throw new IOException("Input file " + inFile.getPath + " not found")
def checkInputBAM(inBAM: File): File = {
private def checkInputBAM(inBAM: File): File = {
// input BAM must have a .bam.bai index
if (new File(inBAM.getPath + ".bai").exists)
checkInputFile(inBAM)
......@@ -141,7 +141,7 @@ object WipeReads {
=> throw new IllegalArgumentException("Unexpected or duplicate option flag: " + option)
}
def validateOption(opts: OptionMap): Unit = {
private def validateOption(opts: OptionMap): Unit = {
// TODO: better way to check for required arguments ~ use scalaz.Validation?
if (opts.get("inputBAM") == None)
throw new IllegalArgumentException("Input BAM not supplied")
......
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