Reload ourselves after purging disk allocation.

The purge process may set a test_name on the object in which case the
lookup_hash will have been modified.  To avoid concurrent modification
reload the object before setting our desired test_name.
Correctly report coordinates and alleles for indels
Reload owner when reloading allocation.

Multiple alignment actions update their owners in the spawned process,
so promptly load the changes to either trigger immediate notification of
conflicts or prevent future changes from causing them.
Whitespace.
Remove unneeded variable.
update coordinates for the deletion test case. Add notes
additional, more complex test cases
Whitespace.
Allow access to the additional columns that were found.
Whitespace.
Rename "ignore_extra_columns" to "allow_extra_columns".

We're not just ignoring them any more!
spelling: preceed* => preced*
Create add_ methods for links to profile items and subject mappings.
Add support for setting tags when creating subject mappings.
Consolidate get() attempts to single statement.
update blessed gene-prediction-bacterial build
Refactor - move coordinate converting code to a utility class
Merge pull request #33 from tmooney/software_result_test_name_collision

Reload the owner after taking action on a disk allocation.
Framework for writing a legend file
Field descriptions for interpreters