v0.8.0

Added

• Deduplication of identical input sequences in every index (FmIndex, BidirFmIndex,
  RlFmIndex, BidirRlFmIndex, MoveFmIndex, BMoveIndex; CPU and GPU builds). Input
  sequences with byte-identical bases (# layout included; headers may differ) form an
  equivalence class, and only the first member, its representative, is stored in the
  text. A sequence that is only a prefix or substring of another is not grouped. SeqIds
  keep their meaning (the position in the builder's input) for every sequence, stored or
  not, and sequence(id) returns any member's bases.
• SeqClasses (seq_classes() on every index) plus equivalence_class(id),
  representative(id) and num_distinct_sequences() accessors.
• Grouped query variants that report a match in a class once, on its representative:
  locate_grouped / locate_rows_grouped (FM, RL, Move), locate_interval_grouped
  (bidirectional indexes), BMoveIndex::locate_grouped, and find_smems_grouped /
  find_mems_grouped (BidirFmIndex, BidirRlFmIndex). BMoveIndex::count_cursor and
  count_fwd(&FwdInterval) (bidirectional indexes) count a cursor's occurrences over every
  member.

Changed

• Breaking (results). A match in a sequence with identical copies is reported once per
  class member: locate, locate_rows, locate_interval, locate_fwd,
  FwdInterval::locate, BMoveIndex::locate, Mem::positions (with locate = true),
  FmIndex::locate_gpu and MemHit::positions (with the index's own seq_boundaries)
  list one hit per member, consecutively and by ascending id, in place of the
  representative's hit. Counts include every member: count, count_interval,
  Mem::match_count, MemHit::match_count and the GPU batch MEM counts (so
  match_count == positions.len() still holds for flat MEMs). Cursor size() and the
  count_*_in / count_wild_* helpers still count the stored text. Inputs without
  identical sequences give the same results as before.
• Breaking. seq_boundaries() (now also on FmIndex), map_position,
  locate_positions(_many), text_len() and BMoveCursor::toehold describe the stored
  (deduplicated) text: boundaries are indexed by stored slot rather than SeqId, and raw
  positions lie in representatives only. find_smems_gpu / find_mems_gpu expand hits
  only when passed the index's own seq_boundaries(); with any other ref_boundaries
  table (e.g. one built in input order from the original sequences) positions are indices
  into that table, one per stored occurrence, not expanded.
• Breaking (files). Format versions "HFM\x04", "HRL\x04" / "HRB\x04" and
  "HMV\x02" / "HBM\x02" store the sequence classes and the duplicate-row count weights.
  Older files still load (every sequence in a class of its own); blobs written by this
  version cannot be read by older builds. Loading now checks every format's sequence
  tables (header count, boundaries ending at the text length), so a corrupt older
  FmIndex file that used to load is now rejected.

Known limitations

• The WASM bindings (FmIndexHandle) return the expanded locate / count results but do
  not yet expose the classes: no seq_classes, equivalence_class, representative,
  num_distinct_sequences or *_grouped variants from JavaScript.