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

biopet-aggregate/copy-src.sh

biopet-aggregate/pom.xml

biopet-aggregate/rm-src.sh

biopet-aggregate/src/.gitignore

pom.xml

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

.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

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

...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

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

public/biopet-extensions/pom.xml

...umc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py

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

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

...s/src/main/scala/nl/lumc/sasc/biopet/extensions/Cat.scala

...main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala

...main/scala/nl/lumc/sasc/biopet/extensions/Cuffquant.scala

.../main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

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

...main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala