Tuple to dataclass

[XLIU-hub]

Pull Request Details

This pull request replaces tuple-based return values with dictionaries across the crossmapper. This change introduces dictionaries with explicit keys, improving:

• Readability of the codebase
• API clarity for users, especially in documentation

For example, instead of:
position, offset, in_cds, in_transcript = func(...)
The API now returns:
pos_m = func(...)
pos_m['position']
pos_m['offset']
pos_m['region']
pos_m['position_in_codon']

Documentation has been updated to reflect these new return types.

Breaking Changes

Functions that previously returned positions in tuples now return dictionaries. This affects downstream code that:

• Relies on tuple unpacking
• Access values by index
• Use position values without considering its region

Tests

• All tests have been updated to reflect dictionary-based return values
• All existing and new tests pass