check SAMRecords' "read unmapped" flag

seems like something we should be looking at when parsing SAMRecords

also a few random other cleanups / nits

this builds on my [other PR](https://github.com/hammerlab/guacamole/pull/152) that splits up `Read.scala`, so diffs may be cleaner once that one has happened.
This test change is due to the flag change correct?  There are two reads that have that flag set?