Fixes for updates from py2 to py3 and due to the increment in pysam version to 0.20.0.
- pysam changed the API term: cigar to cigartuples. Calls were updated to account for this change.
- Mapping of contig names to header positions was off, and required correction.
- g2g.get_logger was used in several places when g2g_utils.get_logger was intended.