Lowering compression level of GATK tools...

... should give some performance benefits, while losing very little in
in terms of file size.
Fixing DNABestPracticeVariantCalling for non-human

This means some perhaps subtle changes. I moved to notHuman option into
the GATKConfig class as this is now used both in variant calling and
data processing. This idea is that now the FileAndProgramResourceConfig
trait will not load the default (human) resource files, and thus defer
them to what's been set on the command line. This should mean that the
human files are not loaded when it goes into the dataprocessing and thus
are not used.
The last value is the flowcell id.

Closes issue #26.
Moving old Setup xml stuff into legacy namespace

Making room for the new stuff.
WIP Fixing setupFileCreator with new format
Some more comments and extra help at exception.
New SetupXMLReader implemented
Adding tests for the new setup reader

I just copied the tests for the legacy reader and made sure that if it
contained the same informtation, the reader would return the same info,
and that seems to be working.
Add test for reader switching
Switch SetupXMLReader by looking for <runfolder>

If this tag is present it will be assumed that this is a file on the
legacy format.
Update the README with new input format
WIP Setting up report generator
WIP Creating report files

Can now get piper, GATK and program version. Still need to get resource
versions.
WIP: report function for DNA_BPVC is done

Still need to add it to the qscript and test it.
Added the report creation to DNA_BPVC
Even empty maps need to return a none-value
Added missing else clause...

Which caused there to always be a empty return
Adding version numbers to uppmax_global_config
Make sure to always send a map with default value
Transcripts and Annotations are the same thing...

... so no need to keep both as far as I can see.