enableRCtrimming is used to enable trimming of Reverse Complement versions of adapters

Make trimming of Reverse complement version of adapters optional (by default enableRCtrimming=false)

See merge request !393

Added scattering on annotation

Fixes #305 and #324 

See merge request !374

Fixed tagged files

Fixes #339 

See merge request !394

Adding more unit tests

Adding some random unit tests on this branch

Also fixes #338 

See merge request !391

Fix gvcfs extract



See merge request !389

Conflicts:
	shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala

Addec config option to disable merging of countfiles



See merge request !392

(cherry picked from commit 9e6a44e1)

Fix vcf filter test

Try to solve #333 with this

See merge request !386