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)

Fix report, the logic to display SE or PE from flexiprep stats is deprecated since we always use flexiprep->cutadapt in SE mode. So only SE mode variables are generated and should be displayed in the report.

Set default htseq-count sorting order to pos



See merge request !364

Release 0.6.0

This is to merge back changes on the release branch to develop again. First !362  should be done

See merge request !363