Merge branch 'develop' into feature-toucan

Conflicts:
	.idea/compiler.xml
	.idea/encodings.xml
	.idea/misc.xml
	.idea/modules.xml
	.idea/scala_compiler.xml
	.idea/vcs.xml
	protected/basty/Basty.iml
	protected/biopet-gatk-extensions/BiopetGatkExtensions.iml
	protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml
	protected/biopet-protected-package/BiopetProtectedPackage.iml
	public/bammetrics/BamMetrics.iml
	public/biopet-framework/BiopetFramework.iml
	public/biopet-public-package/BiopetPublicPackage.iml
	public/flexiprep/Flexiprep.iml
	public/gentrap/Gentrap.iml
	public/mapping/Mapping.iml
	public/sage/Sage.iml
	public/yamsvp/Yamsvp.iml