Refactor some loops and remove warnings

Reimplement some .par, removing for-loops. 
Avoiding warnings from the compiler wining about version specific syntax.

Adding description to the report builder (it's own commandline arg)

See merge request !376

Adding SortVcf extension

This wrapper can be used to sort VCF files, whenever they have to be sorted (some variant callers generate non-sorted VCF).

See merge request !372

Reimplement some .par, removing for-loops. Avoiding warnings from the compiler wining about version specific syntax.

BamUtils Insertsize estimation is more acurate by sampling from all over the contig.

Updated BamUtils to fix the insertsize estimation used in the PindelConfig tool.

See merge request !371

Fixed bug



See merge request !375

Added binominal test

Added this for project 168

See merge request !367

Feature configNamespace

See #163.  

See merge request !348

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

Fix basecounter

Some small fixes

See merge request !373

Fixed bug in vcffilter

Fixes #313 

See merge request !370

(cherry picked from commit f5f2787f)