Feature varscan into shiva

Fixes #246 

See merge request !308

Conflicts:
	public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala

Fix 260

Closes #260 

See merge request !314

This reverts commit 2b618795.

Fixed error message in bamutils

Fixes #259 

See merge request !311

(cherry picked from commit a13b0d1d)

Update Cutadapt wrapper

Updated cutadapt wrapper to reflect cutadapt 1.9 and added missing options (which were already supported in 1.5 but not in extension)

Closes #243 

See merge request !310

Feature core unit tests

Fixes #253 

See merge request !307

Fix renames

Some naming fixes for consistency.

See merge request !309