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

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

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

.../lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala

...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala

.../lumc/sasc/biopet/extensions/gatk/BamGatherFunction.scala

...l/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala

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

.../lumc/sasc/biopet/extensions/gatk/CatVariantsGather.scala

...la/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala

...nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala

...nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala

...c/sasc/biopet/extensions/gatk/ContigScatterFunction.scala

...main/scala/nl/lumc/sasc/biopet/extensions/gatk/Gatk.scala

...umc/sasc/biopet/extensions/gatk/GatkScatterFunction.scala

...umc/sasc/biopet/extensions/gatk/GenotypeConcordance.scala

...a/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala

...nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala

.../nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala

...mc/sasc/biopet/extensions/gatk/LocusScatterFunction.scala

...cala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala