bowtie2-rs

Benchmark-first, lane-by-lane Rust port of Bowtie2.

Status

Early Phase A: low-risk translation units from the C++ codebase are ported with parity checks before aligner/index/SIMD core work. See PORTING.md and .c-to-rust-port/PORT_QUEUE.tsv for the current queue.

Layout

• src/ — Rust crate (bowtie2-rs)
• PORTING.md — port ledger and readiness gates
• CONTEXT.md — parity vocabulary (milestones, matrices, claims)
• .c-to-rust-port/PHASE_II_MATRIX_V1.md — named Phase II parity matrix (v1)
• GOAL.md — unattended Phase A completion criteria
• .c-to-rust-port/ — unit tasks, results, and agent prompts

Upstream Bowtie2 sources are read-only under /home/jake/Projects/bowtie2 during this phase.

Non-goals (for now)

• No claim of production parity with bowtie2 binaries until benchmark fixtures say so.
• No bulk rewrite of FM-index, SIMD, or full aligner paths without semantic export coverage.

License

GPL-3.0-or-later (aligned with Bowtie2).