High-priority TODO list
=======================

Once cigarillo is in Bioconductor:

- Deprecate all CIGAR utility functions defined in GenomicAlignments in
  favor of the new CIGAR utility functions defined in cigarillo.

- Modify the code in GenomicAlignments/R/coordinate-mapping-methods.R
  to use query_pos_as_ref_pos(), ref_pos_as_query_pos(), and
  fast_map_ref_ranges_to_query().
  In particular GenomicAlignments:::.mapToAlignments() should use
  fast_map_ref_ranges_to_query() instead of very inefficient .Call
  entry point "map_ref_locs_to_query_locs" defined in GenomicAlignments.
  Then GenomicAlignments/src/coordinate_mapping_methods.c can go away.


Things to do at BioC 3.22 release time
======================================

- Update README.md


Low-priority TODO list
======================

- Add a general utility (e.g. project_positions()) to project positions from
  an **arbitrary** space (query, reference, or pairwise alignment) to the
  other. The current utilities in R/project_positions.R only allow one to
  project positions from the query space to the reference space, and vice
  versa. This contrasts with the capabilities of project_sequences() which
  allows one to project sequences from an **arbitrary** space to the other.

