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 b682eda9d3c27633c864e38f3b0b9f986bff475a..25a6371be4b3b03976458dd13bb62b26176dd671 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 d67f3651778b857d912a8d233c3189eba5be6e51..ebe393bfab7bdb8fedec024319e99a5b0ec29a07 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 9eeb9fa3cb6ac4b2c1c826054682c7a21fa85d26..ff2303567af0a2c203c3b7b3ea01cbe21037f7fd 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 ade8c28fa9e1de2f2de945ca58dd7b4d94253a9e..476e8e6230caa6bd1051a683459ca28566516699 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 8f78acba776ae28c5988a3c5d026375fedd5101b..ffa8be0bcb6c2cf15bf0ad00efeeb54e903eb3df 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 af0243cdaa8d7ff7391513aac60d2aa1275dbd62..8057c9d2578860d44c1bc56d8f413a1fe534fe31 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 } - }