Adding extract.sh simple tool to convert vcf into easy to work with format for R
Adding script which takes 3 vcfs and makes a venn diagram out of them.
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
Minor script changes
--parameterized makeVenns.R so that it takes accepts a list of files on the command line
--modified makeVennFrom3Plots.sh so that it uses Rscript instead of R.
Merge branch '1v1compare'
--merging in a script to generate a plot from a trio of vcfs
Merge branch 'master' into exome
--another catchup

Conflicts:
	GenerateBenchmark.scala