Merge branch 'develop' into fix-pindel-vcf-dependency

.gitignore

README.md

biopet-aggregate/pom.xml

docs/developer/example-pipeline.md

docs/developer/example-tool.md

docs/developer/scaladocs.md

docs/general/config.md

docs/general/memory.md

docs/index.md

docs/pipelines/bam2wig.md

docs/pipelines/basty.md

docs/pipelines/carp.md

docs/pipelines/flexiprep.md

docs/pipelines/gears.md

docs/pipelines/gentrap.md

docs/pipelines/mapping.md

docs/pipelines/sage.md

docs/pipelines/shiva.md

docs/pipelines/tinycap.md

docs/pipelines/toucan.md