From 40de3b9beda2cfab5cb8f16d0cdee7819c6fe1e0 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 4 Apr 2016 14:02:00 +0200
Subject: [PATCH] Style changes
---
.../main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 5 ++---
1 file changed, 2 insertions(+), 3 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 d73c2a858..4a679d206 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
@@ -159,7 +159,7 @@ object MpileupToVcf extends ToolCommand {
val seqErr = 1.0 - binomial.cdf(value.forward + value.reverse)
maSeqErr match {
case Some(x) if (x < seqErr) =>
- case _ => maSeqErr = Some(seqErr)
+ case _ => maSeqErr = Some(seqErr)
}
format += ("SEQ-ERR" -> (format("SEQ-ERR") + "," + seqErr.toString))
format += ("AFC" -> ((if (format.contains("AFC")) format("AFC") + "," else "") + value.forward))
@@ -170,10 +170,9 @@ object MpileupToVcf extends ToolCommand {
maSeqErr match {
case Some(x) => format += ("MA-SEQ-ERR" -> x)
- case _ =>
+ case _ =>
}
-
if (alt.nonEmpty) {
val ad = for (ad <- format("AD").toString.split(",")) yield ad.toInt
var left = reads - dels
--
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