Custom Alphabets
Matching semantics are pluggable through the Alphabet trait (src/alphabet.rs). Rather
than carrying a generic type parameter, FmIndex and BidirFmIndex store a runtime
AlphabetFns bundle (function pointers plus a serialization tag), so the index type itself
stays alphabet-agnostic while the match rules are chosen at build time.
Built-in alphabets
| Alphabet | Behavior |
|---|---|
IupacDna (default) | Full 16-symbol IUPAC matching — N and other ambiguity codes expand to base-set overlap. Used by build_cpu / build. |
ExactDna | Only A/C/G/T match themselves; any ambiguity code (including N) produces zero hits. Useful for peer-comparable benchmarks where other tools don’t treat N as a wildcard. |
Choosing one
The default build_cpu / build use IupacDna. To pick a different alphabet, use the
_with constructors:
use haystackfm::alphabet::ExactDna;
use haystackfm::{FmIndex, BidirFmIndex};
let index = FmIndex::build_cpu_with::<ExactDna>(&seqs, &config)?;
let bidir = BidirFmIndex::build_cpu_with::<ExactDna>(&seqs, &config)?;Implementing your own
Implement Alphabet for a custom type to define your own symbol set and match rules. The
trait carries a safety contract — stable function pointers and a unique serialization tag
(≥ 128) so serialized indices can be matched back to their alphabet. See the trait docs in
src/alphabet.rs on docs.rs for the exact requirements.