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