Merge remote-tracking branch 'remotes/origin/develop' into feature-more_unit_tests

...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

.../main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala

...scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

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

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

.../src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala

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

.../src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala

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

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

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

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