Fixing an issue in pileup generation and in the MdTag util.

This pull request fixes two co-mingled issues that are seen in reads->reference transformation:
* If there is a mismatch, the read and reference bases were swapped in the pileup.
* The MdTag utility could not handle tags with non-[ATGC] bases.

These errors caused significant issues on some 1000Genomes files.

Additionally, I have added test coverage.