Change setup so it can presume vcf types instead of forcing it to strings. Some style changes. Added support for different inputField and outputField

Conflicts:
	public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

Patch toucan

This enables to `--fork` command of the VEP to actually run with Biopet's `-qsub` command.

See merge request !126

Feature gentrap

See merge request !111

Patch genotyper

Fix a small bug on unified genotyper

See merge request !125

Patch aln wrapper threads

@p.j.van_t_hof, @wyleung, and @a.h.b.bollen ~ for the threads behavior that we saw earlier today

See merge request !124

Feature test coverage

Removed aggregated scoverage module, now not breaking packaging anymore.

See merge request !117

Patch toucan

Fix output directory path in Toucan

See merge request !123

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

Feature shiva

This will become a new version of the variantcalling pipeline.

See also issue #116 and #119

See merge request !110

Feature rcommandline

R commandline function cherry-picked

See merge request !121