Commit 5c0f52d3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style fixes

parent bdadf513
......@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import htsjdk.samtools.reference.IndexedFastaSequenceFile
import nl.lumc.sasc.biopet.core.summary.{SummaryQScript, Summarizable}
import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -135,10 +135,10 @@ object Reference {
* @param fastaFile Fasta file
*/
def requireDict(fastaFile: File): Unit = {
val dict = new File(fastaFile.getAbsolutePath
.stripSuffix(".fna")
.stripSuffix(".fa")
.stripSuffix(".fasta") + ".dict")
val dict = new File(fastaFile.getAbsolutePath
.stripSuffix(".fna")
.stripSuffix(".fa")
.stripSuffix(".fasta") + ".dict")
if (!checked.contains(dict)) {
checked += dict
if (!dict.exists()) Logging.addError("Reference is missing a dict file")
......
......@@ -2,8 +2,8 @@ package nl.lumc.sasc.biopet.core
import java.nio.file.Paths
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import nl.lumc.sasc.biopet.utils.config.{Configurable, Config}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.{ Configurable, Config }
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
......@@ -11,8 +11,8 @@ import org.mockito.Mockito._
import org.testng.annotations.Test
/**
* Created by pjvan_thof on 12/30/15.
*/
* Created by pjvan_thof on 12/30/15.
*/
class ReferenceTest extends TestNGSuite with Matchers with MockitoSugar {
import ReferenceTest._
......@@ -71,7 +71,7 @@ object ReferenceTest {
dict: Boolean = false) = new Reference {
val root = r
override def globalConfig = new Config(configs
.foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b)} )
.foldLeft(Map[String, Any]()) { case (a, b) => ConfigUtils.mergeMaps(a, b) })
override def dictRequired = if (dict) true else super.dictRequired
override def faiRequired = if (fai) true else super.faiRequired
}
......
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