From 2759a09fb8fdc955c37a6eb1cccf7edd52a47f33 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 4 Apr 2016 16:04:57 +0200
Subject: [PATCH] Style changes
---
.../main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 6 +++---
1 file changed, 3 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 4a679d206..5d1b00201 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
@@ -101,7 +101,7 @@ object MpileupToVcf extends ToolCommand {
}
val reads = values(3).toInt
val mpileup = values(4)
- val qual = values(5)
+ //val qual = values(5)
val counts: mutable.Map[String, Counts] = mutable.Map(ref.toUpperCase -> new Counts(0, 0))
@@ -158,8 +158,8 @@ object MpileupToVcf extends ToolCommand {
format += ("AD" -> (format("AD") + "," + (value.forward + value.reverse).toString))
val seqErr = 1.0 - binomial.cdf(value.forward + value.reverse)
maSeqErr match {
- case Some(x) if (x < seqErr) =>
- case _ => maSeqErr = Some(seqErr)
+ case Some(x) if x < seqErr =>
+ case _ => maSeqErr = Some(seqErr)
}
format += ("SEQ-ERR" -> (format("SEQ-ERR") + "," + seqErr.toString))
format += ("AFC" -> ((if (format.contains("AFC")) format("AFC") + "," else "") + value.forward))
--
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