Fix code style warnings

...rc/main/scala/nl/lumc/sasc/biopet/scripts/SquishBed.scala

.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala

.../scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala

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

.../nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala

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

...cala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

...scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

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

...n/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala

...rc/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

...rc/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala

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

...n/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala

...scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala

...in/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala

...rk/src/main/scala/nl/lumc/sasc/biopet/tools/SeqStat.scala

...c/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala