Mutant Maricopa

This release adds an additional parameter --assign_ambiguous_alignements_to_first_allele. For ambiguous alignments, setting this flag will force them to be assigned to the first (as provided by the references -a first and then -e second) amplicon. Thus, no reads will be discarded as 'ambiguous' and all reads will be counted once in the analysis.

In addition, batch summaries are produced for amplicons present in only one sample.