Merge branch 'develop' into fix-svcallers-vcf

biopet-aggregate/pom.xml

.../nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala

...e/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala

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

...c/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala

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

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

...scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala

public/biopet-public-package/pom.xml

...in/scala/nl/lumc/sasc/biopet/BiopetExecutablePublic.scala

...cala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala

...a/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala

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

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

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

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

public/biopet-tools/src/test/resources/VEP_oneline.vcf

public/biopet-tools/src/test/resources/VEP_oneline.vcf.gz

...ic/biopet-tools/src/test/resources/VEP_oneline.vcf.gz.tbi

public/biopet-tools/src/test/resources/gens.samples