Added a bunch of QC code to _orthogroup_index().
Minor cleanup in _genbank_quality_filter.
Fixed bug when updating OG_index after dissolving/creating OGs in merge().
Fixed bugs in merge() when handling ohnologs.
Fixed bug in merge() when handling orthogroups.
Edited wise() to use YGOB_HMMER3_URL env var to get HMMs if available. No longer hard coding S3 url.
Changes to reoptimise() to discard untranslateable errors. Edits in _decompose_gene_name()/_compute_gene_distance() to handle manually supplied HMR/L gene locations.
Fixed bug in fragment() where -return=>score was not being supplied to exonerate2()
Added reset( -hard => 0|1 ) method to erase current evidence and assignments
Corrected reset( -hard => 0|1 ) method to erase current evidence and assignments
Added integrate() method to logically combine ohnologs/orthogroup relations from two models.
Added linked() method to test whether two objects are in the same linkage group. Tests contig and optional distance.
Fixed bug in integrate() and return value in partial()
 Lots of cleanup on merge(). Ignore debugging code in _make_genbank_gene_terminii()...
Small bug fixes and edits in integrate(), _dissolve_orthogroup(), _define_orthogroup().
Just cleaning up...