Merge branch 'develop' into feature-varda

...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala

...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala

.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala

...lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala

...iopet/pipelines/gatk/variantcallers/HaplotypeCaller.scala

...pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala

...t/pipelines/gatk/variantcallers/HaplotypeCallerGvcf.scala

...opet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala

...ipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala

.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

protected/biopet-protected-package/pom.xml

protected/pom.xml

public/LICENSE

public/bam2wig/pom.xml

public/bammetrics/pom.xml

...c/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp

...nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp

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