Remove some test and optimize code

public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/AbstractTestMapping.scala

@@ -15,28 +15,24 @@
  */
 package nl.lumc.sasc.biopet.pipelines.mapping
 
-import java.io.{ File, FileOutputStream }
+import java.io.{File, FileOutputStream}
 
 import com.google.common.io.Files
-import nl.lumc.sasc.biopet.utils.config.Config
-import nl.lumc.sasc.biopet.extensions._
-import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
-import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, SortSam }
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
-import nl.lumc.sasc.biopet.extensions.tools.{ FastqSync, SeqStat }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Config
 import org.apache.commons.io.FileUtils
 import org.broadinstitute.gatk.queue.QSettings
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
-import org.testng.annotations.{ AfterClass, DataProvider, Test }
+import org.testng.annotations.{AfterClass, DataProvider, Test}
 
 /**
  * Test class for [[Mapping]]
  *
  * Created by pjvan_thof on 2/12/15.
  */
-abstract class AbstractTestMapping extends TestNGSuite with Matchers {
+abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Mapping = {
     new Mapping {
       override def configName = "mapping"
@@ -46,13 +42,10 @@ abstract class AbstractTestMapping extends TestNGSuite with Matchers {
     }
   }
 
-  val aligner: String
-
   @DataProvider(name = "mappingOptions")
   def mappingOptions = {
-    val aligners = Array("bwa-mem", "bwa-aln", "star", "star-2pass", "bowtie", "stampy", "gsnap", "tophat")
     val paired = Array(true, false)
-    val chunks = Array(1, 5, 10, 100)
+    val chunks = Array(1, 5)
     val skipMarkDuplicates = Array(true, false)
     val skipFlexipreps = Array(true, false)
     val zipped = Array(true, false)
@@ -100,42 +93,17 @@ abstract class AbstractTestMapping extends TestNGSuite with Matchers {
   }
 }
 
-class MappingBwaMemTest extends AbstractTestMapping {
-  val aligner = "bwa-mem"
-}
-
-class MappingBwaAlnTest extends AbstractTestMapping {
-  val aligner = "bwa-aln"
-}
-
-class MappingStarTest extends AbstractTestMapping {
-  val aligner = "star"
-}
-
-class MappingStar2PassTest extends AbstractTestMapping {
-  val aligner = "star-2pass"
-}
-
-class MappingBowtieTest extends AbstractTestMapping {
-  val aligner = "bowtie"
-}
-
-class MappingStampyTest extends AbstractTestMapping {
-  val aligner = "stampy"
-}
-
-class MappingGsnapTest extends AbstractTestMapping {
-  val aligner = "gsnap"
-}
-
-class MappingTophatTest extends AbstractTestMapping {
-  val aligner = "tophat"
-}
+class MappingBwaMemTest extends AbstractTestMapping("bwa-mem")
+class MappingBwaAlnTest extends AbstractTestMapping("bwa-aln")
+class MappingStarTest extends AbstractTestMapping("star")
+class MappingStar2PassTest extends AbstractTestMapping("star-2pass")
+class MappingBowtieTest extends AbstractTestMapping("bowtie")
+class MappingStampyTest extends AbstractTestMapping("stampy")
+class MappingGsnapTest extends AbstractTestMapping("gsnap")
+class MappingTophatTest extends AbstractTestMapping("tophat")
 
 object MappingTest {
 
-  val aligners = Array("bwa-mem", "bwa-aln", "star", "star-2pass", "bowtie", "stampy", "gsnap", "tophat")
-
   val outputDir = Files.createTempDir()
   new File(outputDir, "input").mkdirs()