From 6035d15b0de8dbd8b40cbe87aeea5d2f61f1277e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 31 Mar 2016 13:32:59 +0200
Subject: [PATCH] Invert to pValue
---
.../main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index a9eef0016..fbe074360 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -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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