The initial mapping code took a conservative approach and discarded "broken" features. This works well for mapping between similar assemblies, but is sub-optimal between more distant species, and potentially interferes with more interesting uses of the mapping infrastructure, such as https://github.com/dasmoth/dalliance/issues/63.
Suggested plan:
[x] Update mapping code to preserve partially mapped features, using attributes (e.g. partialMin and partialMax) to record partial mapping state (WIP by @dasmoth, hopefully done today).
[ ] Visual indication of when you're looking at a partially-mapped feature (maybe needs to be optional?)
[ ] Some special-case code will be needed for sequence-alignment features to make sure that alignment rendering works out after mapping.
The back-end side of this is done now. Partially mapped features have partialMin and/or partialMax attributes indicating how many bases of the partially-mapped feature have been trimmed.
The initial mapping code took a conservative approach and discarded "broken" features. This works well for mapping between similar assemblies, but is sub-optimal between more distant species, and potentially interferes with more interesting uses of the mapping infrastructure, such as https://github.com/dasmoth/dalliance/issues/63.
Suggested plan:
Any other special cases we need?