Patch carp summary fix

In the CARP pipeline we forgot to fill in the global summary file. So this had to be added. Tested and works fine now!

See merge request !115

Patch executable check

See merge request !114

Patch carp

Merge to fix the wrong directory of MACS2 single samples runs

See merge request !113

Patch mutisample summary

See merge request !112

Patch parallel tests

See merge request !109

Patch summary

See merge request !108

Patch macs2 callpeaks

Patch to fix the argument parsing of modelfold in macs2 callpeak. Test succeeded.

See merge request !105

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