Latebreaking additions to workflow to reduce dependancy on dowloading BAMs

NOTE: readme details minor installation changes, particularly which items still need apt-get when pulling pre-compiled code from Artifactory.

Changes to workflow to include:

Gneration of count/gc/allele bin files similar to thouse used in legacy PICNIC NGS tools, these have been found to be usedful for downstram analysis of rearrangments.
Primary benefit is that with these available we should be able to use minor slicing while developing more accuraterearrangment analysis.

Base allele counts files based on impute 1000 genomes loci, this is the only input required for Battenberg and they may be of use to others, sadly not VCF but time constrainsts prevented adding conversion.