Fix merge issues



See merge request !321

fix #273



See merge request !320

Feature measure modules

Fixes #247, #212, #255, #262, #269 and #270 

- [x] Added Measurement trait
- [x] Implement Measurements
 - [x] FragmentsPerGene
 - [ ] Added id sorting for FragmentsPerGene
 - [ ] FragmentsPerExon (Unimplemented in current version, unclear if this is even possible)
 - [x] BasesPerGene
 - [x] BasesPerExon
 - [x] CufflinksStrict
 - [x] CufflinksGuided
 - [x] CufflinksBlind
- [x] Implement Shiva in Gentrap
- [x] Convert Gentrap class
- [x] Cleanup unused classes

See merge request !306

Make inverse of the boolean to fix issue #272

Fixes #272 

See merge request !319

Fix 268

Fixes #268 

See merge request !318

Conflicts:
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala

Feature qiime

Mainly for project 122

See merge request !287