Updates to pool caller scala script due to new paths and cleanup, hop…

…efully with final changes for paper.

Added also R script used to process everything into a couple of ggplot-friendly data frames.
Functionality is basically the same. Enhancements:
-- Add annotation to log axiom and Exome Chip AC along with LOF results for concordance comparisons.
-- General Cleanup.
-- Used base path for files as a variable in case directory structure in gsa-hpprojects changes again.
-- Output also per-pool data by subsetting genotypes per pool and comparing with corresponding genotypes from Axiom, exome chip and omni.
-- Commit R scripts that load all tables and crunch them to analyze them.