Commit e5ccc0cf authored by Peter van 't Hof's avatar Peter van 't Hof

Adding refcalls

parent 85708a4a
......@@ -27,7 +27,7 @@ import scala.math.{ floor, round }
object MpileupToVcf extends ToolCommand {
case class Args(input: File = null, output: File = null, sample: String = null, minDP: Int = 8, minAP: Int = 2,
homoFraction: Double = 0.8, ploidy: Int = 2, seqError: Double = 0.005) extends AbstractArgs
homoFraction: Double = 0.8, ploidy: Int = 2, seqError: Double = 0.005, refCalls: Boolean = false) extends AbstractArgs
class OptParser extends AbstractOptParser {
opt[File]('I', "input") valueName "<file>" action { (x, c) =>
......@@ -54,6 +54,9 @@ object MpileupToVcf extends ToolCommand {
opt[Double]("seqError") action { (x, c) =>
c.copy(seqError = x)
}
opt[Unit]("refCalls") action { (x, c) =>
c.copy(refCalls = true)
}
}
/**
......@@ -172,7 +175,7 @@ object MpileupToVcf extends ToolCommand {
case _ =>
}
if (alt.nonEmpty) {
if (alt.nonEmpty || commandArgs.refCalls) {
val ad = for (ad <- format("AD").toString.split(",")) yield ad.toInt
var left = reads - dels
val gt = ArrayBuffer[Int]()
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment