Merge pull request #154 from hammerlab/adam-upgrade

upgrade to adam 0.13
Merge remote-tracking branch 'origin/master' into reads-pkg
Merge pull request #152 from hammerlab/reads-pkg

split Read.scala (and tests) into separate files
factor out common MateProperties instantiation
check SAMRecord's mapped-read flag in Read parsing

this changes the value expected by one test case, that was arguably
incorrect before
derive Read.isMapped from Read.getMappedOpt
dangling parend ReadSet
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