make MappedRead require an MDTag

today we runtime-assume this "everywhere"; in the future we may
care about non-MD-tagged-mapped-reads, but today we don't so I've
just co-opted the existing MappedRead class to avoid unnecessary
boilerplate around class hierarchies, kryo serialization, etc.
denormalize reference bases to MappedRead

uses assumption that MD tag exists on MappedRead
Remove unnecessary hasMDTag bool from serde
remove redundant/unnecessary hasMDTag filter
Merge pull request #155 from hammerlab/mdt

Make MappedRead require MDTags