Add some more to the test to vcf filter

Fixes #273 

See merge request !324

New tool to validate if paired end sequences are in sync

The tools has been checked with 4 different fastq files and with randomly removing one line. In all cases the tool did what it is supposed to do. Probably some extra features might be build in, but that comes later.

See merge request !317

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