bug fixes in some alignment tests
ignore mutation diagram stderr files in clinseq test diff
Merge branch 'master' of ssh://git/srv/git/genome
Calculate the hash after adding all the inputs.
Add more lookup hashes to software results __defined__.
We need to get the individual results one-at-a-time.
roi_track_name is not optional in AR:Merged:RefCov.t
Changed many ->get to ->get_with_lock

->get_with_lock is appropriate for software_results if expecting a
single result.  This is because it will use the new faster hashing
lookup instead of the old slow queries.
Merge branch 'software_result_hashing' of ssh://git/srv/git/genome into software_result_hashing
Cleanup this result--make optional things that should be, properly make hash.
make SR get_with_lock confess when underspecified
add lookup_hash to stagable SR test
Merge branch 'software_result_hashing' of ssh://git/srv/git/genome into software_result_hashing
fixed bug in which genome model input update would not allow a value to be set to zero
Major clean-up of CnView tool in advance of further refactor
Fixed bug with check of instrument data type checking in clin-seq update-analysis
No combine results appear to have "version" set, so make it optional.
fix expected test count in ID:AR:Bsmap.t
fix SR/Stagable.t
The aligned_reads_sample isn't needed for combine VCFs--it comes from inputs.

Since it's required in the base class, just give it a default value to
satisfy existence.