Merge with develop

...umc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala

.../nl/lumc/sasc/biopet/extensions/tools/BedToInterval.scala

...sc/biopet/extensions/tools/BedtoolsCoverageToCounts.scala

...nl/lumc/sasc/biopet/extensions/tools/BiopetFlagstat.scala

.../nl/lumc/sasc/biopet/extensions/tools/FastqSplitter.scala

...cala/nl/lumc/sasc/biopet/extensions/tools/FastqSync.scala

...a/nl/lumc/sasc/biopet/extensions/tools/MergeAlleles.scala

...la/nl/lumc/sasc/biopet/extensions/tools/MergeTables.scala

...a/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala

...la/nl/lumc/sasc/biopet/extensions/tools/PrefixFastq.scala

...nl/lumc/sasc/biopet/extensions/tools/SageCountFastq.scala

...lumc/sasc/biopet/extensions/tools/SageCreateLibrary.scala

...mc/sasc/biopet/extensions/tools/SageCreateTagCounts.scala

.../scala/nl/lumc/sasc/biopet/extensions/tools/SeqStat.scala

...cala/nl/lumc/sasc/biopet/extensions/tools/SquishBed.scala

...cala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala

...scala/nl/lumc/sasc/biopet/extensions/tools/VcfStats.scala

...ala/nl/lumc/sasc/biopet/extensions/tools/VcfWithVcf.scala

.../nl/lumc/sasc/biopet/extensions/tools/VepNormalizer.scala

...cala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala