Feature scoverage

In this merge I try to fix #123 and #37

See merge request !240

(cherry picked from commit 8bf162ad)

Fix chunking

Chunking was broken in develop, this should fix it

See merge request !250

Feature filter on mapping quality carp

Currently testing the pipeline with real samples. Dry run seem to look okay!

Pipeline tested, ready to merge!

See merge request !248

# Conflicts:
#	public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

Fix flexiprep

Fixing some small issue here found in integration tests.

See merge request !247

Feature fixed values

See #126 

Order of prio of config values:
1. Fixed values
2. User config (-config / -cv on the command line)
3. Default files (coming from BIOPET_CONFIG env)
4. Default values inside the code.

Also changed way to use default values. No need for a merge step anymore, this happens inside the class now. This makes code inside pipelines/extensions cleaner.

Todo:
- [x] Basic implementation
- [x] Unit testing

See merge request !233

Fix errornous foldername

moves folder public/biopet-extentsions -> public/biopet-extensions

See merge request !244

Feature pipeable

Fixes #114 

See merge request !234