running UnifiedGenotyper on each spiked bam to calculate readDepths and alleleFractions for each variant position
Added new AltReadFraction stratification module for varianteval
--It stratifies by alternate allele read fraction
--Edited the SomaticSpike xml files to force it to be included in the build/packaging
Merge branch 'master' into calcAlleleFraction

Merging fix to SomaticSpike invocation.

Conflicts:
	GenerateBenchmark.scala
Added scripts to generate a graph of readFraction distributions
--runeval.sh runs VariantEval on a set of the genotype spikein vcfs
--Adding R script plotAltReadFraction.R to create a graph of readFraction distributions.
--currently both are hard coded and bad
Adding average lines from the plot of AltReadFraction.R
Merge branch 'calcAlleleFraction'
--moving read fraction scripts into master.
--these must be run manually at the moment