Patch coniferfix

There was a bug in reading files from the RPKM ref directory.

Now filters to *.txt and the .out file is now created as a hidden file (for inprocess runs we need to overrride this)

Reporter: Gijs Santen,
Fix: Wai Yi Leung

See merge request !93

Flexiprep unit test + fix for small bugs

See subject

See merge request !94

Conflicts:
	protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
	public/mapping/pom.xml

Feature bam to big wig

feature ready for merge, see also #86

See merge request !92