From 9b8e7dd8f436496f9606036a22ae1dbc421c921b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 1 Aug 2015 15:07:14 +0200
Subject: [PATCH] Fix inspection warnings
---
.../nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 8774bdc98..ccd47d551 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
@@ -35,7 +35,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
var inputVCF: File = _
def init(): Unit = {
-
}
override def defaults = ConfigUtils.mergeMaps(Map(
@@ -63,28 +62,26 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
var outputFile = normalizer.outputVcf
gonlVcfFile match {
- case Some(gonlVcfFile) => {
+ case Some(gonlFile) =>
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = outputFile
- vcfWithVcf.secondaryVcf = gonlVcfFile
+ vcfWithVcf.secondaryVcf = gonlFile
vcfWithVcf.output = swapExt(outputDir, normalizer.outputVcf, ".vcf.gz", ".gonl.vcf.gz")
vcfWithVcf.fields ::= ("AF", "AF_gonl", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
- }
case _ =>
}
exacVcfFile match {
- case Some(exacVcfFile) => {
+ case Some(exacFile) =>
val vcfWithVcf = new VcfWithVcf(this)
vcfWithVcf.input = outputFile
- vcfWithVcf.secondaryVcf = exacVcfFile
+ vcfWithVcf.secondaryVcf = exacFile
vcfWithVcf.output = swapExt(outputDir, outputFile, ".vcf.gz", ".exac.vcf.gz")
vcfWithVcf.fields ::= ("MAF", "MAF_exac", None)
add(vcfWithVcf)
outputFile = vcfWithVcf.output
- }
case _ =>
}
}
--
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