Sync with develop and fix build issues

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala

.../test/scala/nl/lumc/sasc/biopet/core/BiopetPipeTest.scala

...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