Merge branch 'develop' into feature-FilterOnMappingQualityCarp

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Star.scala

...src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.scala

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

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

...in/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

.../src/main/scala/nl/lumc/sasc/biopet/extensions/Zcat.scala

...la/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala

...l/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala

...la/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala

...mc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

...umc/sasc/biopet/extensions/bedtools/BedtoolsGroupby.scala

...c/sasc/biopet/extensions/bedtools/BedtoolsIntersect.scala

...lumc/sasc/biopet/extensions/breakdancer/Breakdancer.scala

...asc/biopet/extensions/breakdancer/BreakdancerCaller.scala

...asc/biopet/extensions/breakdancer/BreakdancerConfig.scala

...c/sasc/biopet/extensions/breakdancer/BreakdancerVCF.scala

...c/main/scala/nl/lumc/sasc/biopet/extensions/bwa/Bwa.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala

...ain/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala

...n/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala