Fixed error setting GAP evidence data in _validate_assembly_gaps(). Added missing index() call.
_genbank_quality_filter() added code to hide small orfs from GBK. Should be managing in _make_genbank_gene_terminii(). Time bomb. Added comments.
Added interruptions() method to return number of non-intron reading frame interrptions. Fixed no upper bound error in introns() method.
Added second iteration of _validate_overlapping_features() to _make_genbank_compatible() to handle case where we merge successfully across introns. Not elegant.
Rewrote and toughened _validate_overlapping_features(). Added minor change to _genbank_quality_filter() to handle short genes.
Bug fix related to frame restoration in _validate_overlapping_features().
Added genbank_exclude() method.
Minor cleanup.
Removed _sort_overlapping annotations.
Replaced ->data( _EXCLUDE_FROM_GENBANK) with new genbank_exclude() method calls.
Bug fixes and small changes in _validate_assembly_gaps()
_make_genbank_compatible() moved merge() method calls to $contig->_validate_overlapping_features().
_validate_overlapping_features() split into validation code and _genbank_gap_overlaps() to make modifications per Genbank needs. Logically cleaner at top level but still messy implementation.
Added excise_gaps() to ensure that exons do not contain any assembly gaps. We create fake "exons" on either side.
Added merge() call to _validate_overlapping_features(). Added excide_gaps() call to _genbank_gap_overlaps().
Created fission() method to split an ORF object into two objects. Fixes to excise_gaps().
Fixes to excise_gaps().
Fixed logic in excise_gaps() and made minor changes in fission().
New logic in _genbank_gap_overlaps() to leverage excise_gaps() and fission(). Ensures no internal overlaps with gaps (e.g., exons) and splits genes in two where required.
Cleaning out debugging cruft in _make_genbank_compatible()