Merge branch 'develop' into feature-option_keep_files_flexiprep

...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala

...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala

.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala

...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

...rces/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R

.../main/resources/nl/lumc/sasc/biopet/scripts/bed_squish.py

.../main/resources/picard/analysis/baseDistributionByCycle.R

...pet-framework/src/main/resources/picard/analysis/gcBias.R

.../src/main/resources/picard/analysis/insertSizeHistogram.R

...k/src/main/resources/picard/analysis/meanQualityByCycle.R

...main/resources/picard/analysis/qualityScoreDistribution.R

...ework/src/main/resources/picard/analysis/rnaSeqCoverage.R

...pet-framework/src/main/resources/picard/analysis/rrbsQc.R

...umc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

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

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

...rc/main/scala/nl/lumc/sasc/biopet/extensions/Tophat.scala

.../nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala

.../scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala

.../main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala