Bioinformatics Pattern Matching Engine

A deterministic, sanitizer-clean, dependency-free C++20 sequence-alignment engine that an in-house team can drop into a pipeline and run in front of regulators the same day. Index files are bit-identical across machines and runs, and every index embeds a SHA-256 manifest of its input — a single command confirms an index was built from the FASTA you think it was.

It answers two problems the open-source incumbents don't. Reproducibility: deterministic builds and a content-hashed, versioned on-disk format that survives a regulatory audit. Scale on similar genomes: a pangenome-aware index that scales with the similarity of the input, not the number of genomes — up to 2.5× less RAM on near-identical references. Exact pattern search runs roughly 2,000× faster than the C++ standard library's substring search, sub-microsecond per query, independent of reference size.

The same engine is exposed through a C++20 native API, a stable C ABI, and a pure-ctypes Python binding, so it integrates from a Rust CLI to a Jupyter notebook to a regulated clinical pipeline. Delivered as proprietary source — engine, C ABI, Python wrapper, command-line tool, test and benchmark suites, and a fuzz-hardened loader — with no third-party runtime dependency beyond libpthread.