Merge branch 'fixsamtofastq' into 'develop'

Fixsamtofastq

Added java GC options to DEVELOP

See merge request !48

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

@@ -5,6 +5,10 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
   executable = "java"
 
+  javaGCThreads = config("java_gc_threads")
+  javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
+  javaGCTimeLimit = config("java_gc_timelimit")
+
   override def afterGraph {
     memoryLimit = config("memory_limit")
   }