Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-seqstat-scala

.idea/compiler.xml

.idea/encodings.xml

.idea/libraries/Maven__nl_lumc_sasc_Bam2Wig_0_3_0_DEV.xml

.idea/modules.xml

.idea/scala_compiler.xml

docs/config.md

log4j.properties

protected/basty/Basty.iml

...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala

protected/basty/src/test/resources/log4j.properties

...lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala

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

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

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

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

.../sasc/biopet/extensions/gatk/RealignerTargetCreator.scala

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

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

...iopet-gatk-extensions/src/test/resources/log4j.properties

protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml