merge change to extract_haplotype_read_counts.py from development branch
merge change to extract_haplotype_read_counts.py from development branch

smozaffari/WASP,gmcvicker/WASP,gmcvicker/WASP,gmcvicker/WASP,bmvdgeijn/WASP,bmvdgeijn/WASP,bmvdgeijn/WASP,smozaffari/WASP,bmvdgeijn/WASP,smozaffari/WASP,smozaffari/WASP,TheFraserLab/Hornet,gmcvicker/WASP,smozaffari/WASP