From 6638216be669c712883ba4651e799a823ffcc790 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 27 Aug 2015 18:04:15 +0200
Subject: [PATCH] Various style fixes

---
 .../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala   | 2 +-
 .../nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala     | 1 -
 .../scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala   | 2 +-
 .../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala   | 2 +-
 .../scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala    | 2 --
 .../nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala      | 3 +--
 6 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index b682eda9d..25a6371be 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.{ File, PrintWriter }
 
-import htsjdk.samtools.{SAMSequenceRecord, SamReaderFactory}
+import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
 import htsjdk.samtools.reference.IndexedFastaSequenceFile
 import htsjdk.variant.variantcontext.VariantContext
 import htsjdk.variant.vcf.VCFFileReader
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
index d67f36517..ebe393bfa 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -65,7 +65,6 @@ class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers
     val father = mock[Args]
     when(father.sampleName) thenReturn "Father_7006506"
 
-
     getMaxAllele(record)(child) shouldBe "C-"
     getMaxAllele(record)(father) shouldBe "CA"
 
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
index 9eeb9fa3c..ff2303567 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstatTest.scala
@@ -33,7 +33,7 @@ class BiopetFlagstatTest extends TestNGSuite with MockitoSugar with Matchers {
   processor.loadRecord(record)
 
   @Test
-  def testReport()= {
+  def testReport() = {
     processor.report shouldBe Source.fromFile(report).mkString
   }
 
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
index ade8c28fa..476e8e623 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import java.nio.file.Paths
 
-import htsjdk.samtools.{SamReaderFactory, SamReader}
+import htsjdk.samtools.{ SamReaderFactory, SamReader }
 import htsjdk.variant.vcf.VCFFileReader
 import org.scalatest.Matchers
 import org.scalatest.mock.MockitoSugar
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
index 8f78acba7..ffa8be0bc 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSplitterTest.scala
@@ -36,6 +36,4 @@ class FastqSplitterTest extends TestNGSuite with MockitoSugar with Matchers {
     main(args)
   }
 
-
-
 }
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
index af0243cda..8057c9d25 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBioTest.scala
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.tools
 import java.io.File
 import java.nio.file.Paths
 
-import htsjdk.samtools.{SamReaderFactory, QueryInterval}
+import htsjdk.samtools.{ SamReaderFactory, QueryInterval }
 import nl.lumc.sasc.biopet.tools.FastqSplitter._
 import org.scalatest.Matchers
 import org.scalatest.mock.MockitoSugar
@@ -60,5 +60,4 @@ class FindRepeatsPacBioTest extends TestNGSuite with MockitoSugar with Matchers
     result.ins shouldEqual Nil
   }
 
-
 }
-- 
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