Feature gatk jar

Added option for selecting jar file for gatk. Possible to tun older versions now

See merge request !50

Feature fix single sample

MERGE please!

See merge request !49

Fixsamtofastq

Added java GC options to DEVELOP

See merge request !48

Feature merge alleles

Extends from !44
Also added a tool MergeAlleles and implemented in the gatk-variantcalling pipeline

See merge request !46

Feature fixbedtools cov stats

Please merge!@!@!
See also #68

See merge request !47

Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala

Feature sample config create

TsvToJson parsen, see also #66

See merge request !45

Patch intellij update

Calling this `patch-` since this is not a feature on the code at all.

Anyway, this updates the project files so they are compatible with the latest release.

See merge request !43