Feature vcfwithvcf

See merge request !143

Conflicts:
	public/biopet-public-package/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutablePublic.scala

Feature vcf with vcf peter

Needed this tool for data that must be ready this Monday. While running this I found some issues that i fixed in this branch:
- Type is kept from secondary vcf file, this makes filtering later much easier.
- Field in secondary vcf can be different as in output vcf, otherwise records can overritten
- raise errors when field already exist in input vcf or field are missing in secondary vcf
- Style changes, lot of var names with '_', converted to camelCaps

See merge request !138

Feature auto memory

Implementation for #136, not yet tested but this should work I think.

See merge request !139

Feature gentrap docs

As we discussed earlier, this is the docs addition to Gentrap and other tools that it uses. I think this should make all the docs for ScalaDoc complete (for the tools I've written).

Please let me know if that is not the case :) ~ so I can add them.

See merge request !141

Patch versioning

For issue #143

See merge request !140

Change setup so it can presume vcf types instead of forcing it to strings. Some style changes. Added support for different inputField and outputField

Feature vcfstats

Adding new functions to vcf stats:
* [x] improved sample allele overlap
* [x] report bin stats in wiggle tracks
* [x] adding sample distribution files

See merge request !134

Patch varscan

This pull request fixes an error caused by incorrect passing of the Java flags to the VarScan command used in Gentrap. For local runs, it has no effect. However, these are important for cluster runs.

See merge request !137

Patch flexiprep

found bug in flexiprep, seqstat can't find fastq when input fastq (extracted by zcat) is removed because only input is the link file from seqtk.

Is this hot fix worthy? I not sure but it could be a blocking bug.

See merge request !136