Rename afterGraph to beforeGraph

...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala

...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala

...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala

...l/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala

...ala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

...lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Raxml.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/RunGubbins.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala

...l/lumc/sasc/biopet/extensions/conifer/ConiferExport.scala

.../lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

.../nl/lumc/sasc/biopet/extensions/macs2/Macs2CallPeak.scala

.../sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

...c/biopet/extensions/picard/CollectInsertSizeMetrics.scala

...l/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala