Merge branch 'develop' into fix-vcfstats-summary

.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala

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

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

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

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

docs/pipelines/tinycap.md

.../sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp

...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingle.scala

...nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala

...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

.../biopet/pipelines/gentrap/measures/FragmentsPerGene.scala

...a/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala

...scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCap.scala