Merge branch 'feature-wipereads' into 'develop'

Feature wipereads enhancements + quicker testing

Lots of internal refactors (mainly because of GATK 3.3 updates, but also to reduce code repetition by using more of `htsjdk`'s already defined functions).

Also, no more `null`s and testing is now faster :face_with_look_of_triumph: !

See merge request !27