GitLab

fails, the feature is reconstructed from transforms of the unagpped
components of the feature
- Added some checks to Transcript/Exon transform that warns and skips
supporting features that do not transform successfully

Added optional argument to get_all_DBEntries and get_all_DBLinks which is the database name. Use like in sql statment so percentage sign can be used for wild cards etc.

Bug fix: is_known() was returning true if the transcript had a display_xref set, which is both incorrect and inconsitent with the is_known() method in Gene.pm. New behaviour is to return true if the transcript's status is KNOWN.

Modifed get_all_DBLinks to sort xrefs by priority (desc), external db name (asc), display_id (asc) before returning them.

Allow to create objects with undefined or unmapped exons (for keeping track of unmapped exons in AlignSlices)

Transcripts.