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

...umc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp

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

biopet-core/pom.xml

...c/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala

...n/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

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

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

...l/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala

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

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

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

...n/scala/nl/lumc/sasc/biopet/extensions/hisat/Hisat2.scala

...la/nl/lumc/sasc/biopet/extensions/hisat/Hisat2Build.scala

...asc/biopet/extensions/picard/CollectMultipleMetrics.scala

...asc/biopet/extensions/qiime/PickClosedReferenceOtus.scala

.../sasc/biopet/extensions/qiime/PickOpenReferenceOtus.scala

...la/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala

biopet-extensions/src/test/resources/ref.fa.fai

...t/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala

...main/scala/nl/lumc/sasc/biopet/BiopetExecutableMain.scala