bugfixes in bed conversion and bam handling
changing default to be more convenient
Add a data type for the "subject" property.
set subject to be of type Genome::Sample on reference alignment, so that listers can reliably query by patient.common_name, etc.
Merge branch 'master' of ssh://git/srv/git/genome
this probably ought to go into Genome::DataSource::RDBMS, but i will refactor after postgres migration is done
Fixed multiple Conequence logic error
Merge branch 'master' of ssh://git/srv/git/genome
work with Sets that store their aggregate values in the old and new places

UR::Object::Set is getting refactored to handle aggregates more efficiently.
Before it can get deployed, the Genome code need to work with both the old
and new Set code