Added config resource ddg2p_deprecated_hgnc.txt to Makefile for inclusion
added script to compare the clinical-filtering output between different analysis runs
fixed bug when extracting allele frequency for a variant for a population

This only affects variants with multiple alternate alleles, where different
allele frequencies are provided for each aleternate allele.:w
Previously this only obtained the first allele frequency found for a population
e.g. "0.01" from "0.01,.,0.05", and now it obtains the highest allele frequency
available for the population.
sha1 hash uses less memory
Merge branch 'master' of ssh://git.internal.sanger.ac.uk/repos/git/ddd/clinical-filter
improved filtering of de novos and compound hets

 - bypass low_VQSLOD FILTER field failure for de novos
 - remove compound hets when one of the pair is polyphen=benign
   unless the benign variant is de novo
 - refactored code for filtering variants
 - removed --tag and --filter options
fix minor bugs with previous commit
check if variant is within known genes by examining overlap between gene and variant positions