Patch meta in summary

This pull request adds a `meta` entry to the root of each summary JSON file. The contents of the meta is:

`last_commit_hash`: the commit hash of the repository when the JAR was built. If the repository has uncommitted changes, `-dirty` is appended to the commit hash.

`pipeline_version`: the version of the pipeline (the one we put in the `pom.xml` file).

This information is static across all modules and subpipelines to any given pipeline run, so I decided to put this in the root.

See merge request !144

Patch extractalignedfastq

The changeset + commit message should be clear enough :). This was caused by a passing a wrong variable to the `BasicFastqWriter` constructor.

See merge request !142

Fix intervals

Fix for #128

See merge request !145

Feature yaml support

Issue #142

Now implemented a yaml parser and commandline argument to add values to config. Json still uses the old parser, when a file extension is ".yaml" the new parser is used. Later we might remove the old parser completely since SnakeYaml also supports json.

See merge request !146

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