Commit 6035d15b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Invert to pValue

parent 38824296
......@@ -150,11 +150,11 @@ object MpileupToVcf extends ToolCommand {
format += ("RFC" -> counts(ref.toUpperCase).forward.toString)
format += ("RRC" -> counts(ref.toUpperCase).reverse.toString)
format += ("AD" -> (counts(ref.toUpperCase).forward + counts(ref.toUpperCase).reverse).toString)
format += ("SEQ-ERR" -> binomial.cdf(counts(ref.toUpperCase).forward + counts(ref.toUpperCase).reverse).toString)
format += ("SEQ-ERR" -> (1.0 - binomial.cdf(counts(ref.toUpperCase).forward + counts(ref.toUpperCase).reverse)).toString)
if (reads >= commandArgs.minDP) for ((key, value) <- counts if key != ref.toUpperCase if value.forward + value.reverse >= commandArgs.minAP) {
alt += key
format += ("AD" -> (format("AD") + "," + (value.forward + value.reverse).toString))
format += ("SEQ-ERR" -> (format("SEQ-ERR") + "," + binomial.cdf(value.forward + value.reverse).toString))
format += ("SEQ-ERR" -> (format("SEQ-ERR") + "," + (1.0 - binomial.cdf(value.forward + value.reverse)).toString))
format += ("AFC" -> ((if (format.contains("AFC")) format("AFC") + "," else "") + value.forward))
format += ("ARC" -> ((if (format.contains("ARC")) format("ARC") + "," else "") + value.reverse))
format += ("FREQ" -> ((if (format.contains("FREQ")) format("FREQ") + "," else "") +
......
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