Feature toucan

See merge request !70

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

Conflicts:
	public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

Patch flagstat dirs

This fixes the recent update of `ouputDir` from `String` to `File`. There are some `apply` method that are overloaded with both `String` and `File`, causing the pipeline to spew out weird error messages.

@p.j.van_t_hof ~ this is what was causing the weird error earlier.

See merge request !101

Patch ide files

This patch excludes existing IDE-specific files from the git index. I'm not sure yet if this solution works clean for everybody, so please test it first locally.

@wyleung & @p.j.van_t_hof , this is what we discussed earlier with the `*.iml` files and `.idea/*` files.

See merge request !98