Feature fix disable mpileup

Small change in pipeline to skip raw caller

See merge request !53

Conflicts:
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
	biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

Feature no output test

For #58

See merge request !52

Feature basty generate fasta

for #31

See merge request !51

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

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

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