Feature fix mapping

Fix for #108

See merge request !81

Feature fix only sample

Fix for #109

Also added addMultiSampleJobs method.

Not sure but maybe method addPerSampleJobs need a new name but just don't know what.

See merge request !79

Feature chipcap

CArp pipeline can be merged into develop!

See merge request !77

Conflicts:
	public/biopet-public-package/pom.xml
	public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

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

Feature cnvpipeline - including changing the PythonCommandLineFunction

CNV pipeline - starts with bamfile

Tickets:

#106
#107

Work for KG

See merge request !76

Feature typofixes

Some small fixes..

Wrapper update *(bwa) and Mapping pipeline..

See merge request !78

Feature fastq sync

For issue #35 :).

See merge request !75