Merge branch 'develop' into fix-svcallers-vcf

bam2wig/pom.xml

bam2wig/src/test/resources/empty.bam

...sc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala

...in/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

...cala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala

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

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

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

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

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

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

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

...ain/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala

...cala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala

...rc/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala

...scala/nl/lumc/sasc/biopet/utils/summary/SummaryTest.scala

.../nl/lumc/sasc/biopet/utils/summary/SummaryValueTest.scala

.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala

.../pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala