v0.1.2

What's Changed

• chore: rename workspace bwa-mem2-rs → bwa-mem3-rs by @nh13 in #7
• ci: switch publish.yml to fg-labs-bot App pattern by @nh13 in #14
• chore(vendor): refresh bwa-mem3 to 85d3b3b3 by @nh13 in #11
• feat(shm): expose shared-memory index lifecycle by @nh13 in #12
• feat(py): Python bindings via pyo3 + maturin by @nh13 in #13
• chore(vendor): refresh bwa-mem3 to v0.2.0 by @nh13 in #16
• ci(pypi): publish wheels to PyPI on GitHub release by @nh13 in #17
• test(py): expand Python API coverage with PhiX fixture + CI integration job by @nh13 in #18
• chore(vendor): refresh bwa-mem3 to v0.2.2 (92d1bcf) by @nh13 in #20
• fix(index): return Err on missing index instead of aborting the process by @nh13 in #21
• chore: release v0.1.2 by @fg-labs-bot[bot] in #15

New Contributors

• @fg-labs-bot[bot] made their first contribution in #15

Full Changelog: v0.1.1...v0.1.2

bwa-mem3-rs v0.1.1

Renamed from bwa-mem2-rs → bwa-mem3-rs

Inaugural release of the renamed workspace, mirroring upstream's rename of fg-labs/bwa-mem2 → fg-labs/bwa-mem3. Crates published to crates.io:

• bwa-mem3-sys — low-level FFI + vendored upstream + custom shim
• bwa-mem3-rs — safe Rust API
• bwa-mem3-rs-cli — bwa-rs thin CLI

Migrating from bwa-mem2-rs

Drop-in replacement at the source level. In Cargo.toml:

# before
bwa-mem2-rs = "0.1.1"
# after
bwa-mem3-rs = "0.1.1"

In Rust:

// before
use bwa_mem2_rs::{BwaIndex, MemOpts /* … */};
// after
use bwa_mem3_rs::{BwaIndex, MemOpts /* … */};

Env vars rename BWA_MEM2_* → BWA_MEM3_*. The links key is now bwa-mem3.

The previously published bwa-mem2-{sys,rs,rs-cli} v0.1.1 crates remain on crates.io as the final release of the old namespace; no plans to yank.

What's in this v0.1.1 (carried forward from bwa-mem2-rs v0.1.1)

bwa-mem3-sys

• Refresh upstream to e80765b + adopt upstream helpers (#6)
• Cache ref_string on the index handle, borrow per-batch (#5)
• Emit 0x2 (proper pair) and 0x10 (self reverse) flags (#4)
• Per-crate READMEs for crates.io landing pages (#2)

bwa-mem3-rs

• Per-crate READMEs for crates.io landing pages (#2)

bwa-mem3-rs-cli

• Emit 0x2 (proper pair) and 0x10 (self reverse) flags (#4)
• Per-crate READMEs for crates.io landing pages (#2)

Tag note

The legacy v0.1.1 tag (no prefix) still points at the final bwa-mem2-* release commit (c206a60); this prefixed tag (bwa-mem3-rs-v0.1.1) inaugurates the bwa-mem3-* line. Future workspace releases follow the prefixed convention.

v0.1.1

What's Changed

• docs: add per-crate READMEs so crates.io renders a landing page by @nh13 in #2
• docs: add CI, crates.io, docs.rs, and license badges to workspace README by @nh13 in #3
• fix(shim): emit 0x2 (proper pair) and 0x10 (self reverse) flags by @nh13 in #4
• feat: refresh bwa-mem2 to e80765b + adopt upstream helpers by @nh13 in #6
• refactor(shim): cache ref_string on the index handle, borrow per-batch by @nh13 in #5
• chore: release v0.1.1 by @github-actions[bot] in #1

New Contributors

• @nh13 made their first contribution in #2
• @github-actions[bot] made their first contribution in #1

Full Changelog: https://github.com/fg-labs/bwa-mem2-rs/commits/v0.1.1