Patch summary md5

Fix on md5 in summary

See merge request !107

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