Patch bowtie

Fix error on paired end reads for bowtie

See merge request !106

Feature summary

* [x] Init version of summary framework
* [x] Add framework to Gatkpipeline / BamMetrics/ Flexiprep / Mapping / Carp
* [x] Convert old summary methods for flexiprep
* [x] Add summary methods for bammetrics
* [x] Add summary methods for mapping (most of this comes from BamMetrics)
* [x] Add documentation for summary
* [x] Add documentation for Flexiprep
* [x] Add documentation for Mapping
* [x] Add documentation for BamMetrics

Complex pipelines like Gatk-pipeline, Carp, Yamsvp and Gentrap need to wait on those summaries. When implemented only the frame work they will grow when metrics and flexiprep also grows.

See merge request !99

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Seqstat.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepSummary.scala
	public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

Feature seqstat scala

Another quick fix for the outDir

See merge request !103

Feature seqstat scala

#34

Ready for testing

See merge request !90

Patch sampletsvtojson

Fix for #117

See merge request !102

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