Split into separated files

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala

+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Script for sv caler Breakdancer */
+class Breakdancer(val root: Configurable) extends SvCaller {
+  def name = "breakdancer"
+
+  def biopetScript() {
+    //TODO: move minipipeline of breakdancer to here
+    for ((sample, bamFile) <- inputBams) {
+      val breakdancerDir = new File(outputDir, sample)
+      val breakdancer = Breakdancer(this, bamFile, breakdancerDir)
+      addAll(breakdancer.functions)
+    }
+  }
+}

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala

+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Script for sv caler Clever */
+class Clever(val root: Configurable) extends SvCaller {
+  def name = "clever"
+
+  def biopetScript() {
+    //TODO: check double directories
+    for ((sample, bamFile) <- inputBams) {
+      val cleverDir = new File(outputDir, sample)
+      val clever = CleverCaller(this, bamFile, cleverDir)
+      add(clever)
+    }
+  }
+}

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala

+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
+
+import nl.lumc.sasc.biopet.extensions.delly.Delly
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/** Script for sv caler delly */
+class Delly(val root: Configurable) extends SvCaller {
+  def name = "delly"
+
+  def biopetScript() {
+    //TODO: Move mini delly pipeline to here
+    for ((sample, bamFile) <- inputBams) {
+      val dellyDir = new File(outputDir, sample)
+      val delly = Delly(this, bamFile, dellyDir)
+      delly.outputName = sample
+      addAll(delly.functions)
+    }
+  }
+}

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala

 package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
-import java.io.File
-
 import nl.lumc.sasc.biopet.core.{Reference, BiopetQScript}
-import nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
-import nl.lumc.sasc.biopet.extensions.clever.CleverCaller
-import nl.lumc.sasc.biopet.extensions.delly.Delly
-import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /**
@@ -24,44 +18,8 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
   def init() = {}
 }
 
-class Breakdancer(val root: Configurable) extends SvCaller {
-  def name = "breakdancer"
 
-  def biopetScript() {
-    //TODO: move minipipeline of breakdancer to here
-    for ((sample, bamFile) <- inputBams) {
-      val breakdancerDir = new File(outputDir, sample)
-      val breakdancer = Breakdancer(this, bamFile, breakdancerDir)
-      addAll(breakdancer.functions)
-    }
-  }
-}
 
-/** default mode of bcftools */
-class Clever(val root: Configurable) extends SvCaller {
-  def name = "clever"
 
-  def biopetScript() {
-    //TODO: check double directories
-    for ((sample, bamFile) <- inputBams) {
-      val cleverDir = new File(outputDir, sample)
-      val clever = CleverCaller(this, bamFile, cleverDir)
-      add(clever)
-    }
-  }
-}
 
-/** Makes a vcf file from a mpileup without statistics */
-class Delly(val root: Configurable) extends SvCaller {
-  def name = "delly"
 
-  def biopetScript() {
-    //TODO: Move mini delly pipeline to here
-    for ((sample, bamFile) <- inputBams) {
-      val dellyDir = new File(outputDir, sample)
-      val delly = Delly(this, bamFile, dellyDir)
-      delly.outputName = sample
-      addAll(delly.functions)
-    }
-  }
-}