Added a script count_haplotypes.pl to take translated reads (output of convert_reads_to_amino_acid.pl), extract amino acids at particular positions and tally the motifs up across multiple files.
Added license information and third-party software references.
Fixed a bug in get_majority_block_bam (thanks to @jrkirk61 for reporting!)
Added logic to handle a situation where all residues at a position are ambiguous.
Added a new option to compute_cutoff script to allow the user to specify an acceptable minimum threshold primerID group size.