Patch shiva

See merge request !131

Fix markduplicates to not overwrite bam file with metrics file

Patch bam2wig

See merge request !128

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