Crate bwa_mem2_rs 

Safe Rust API for bwa-mem2 alignment.

This crate exposes bwa-mem2 alignment through a blocking, reentrant per-batch API with packed BAM output. Callers own all parallelism — every function is synchronous on its calling thread and safe to call concurrently from multiple threads sharing the same BwaIndex.

Phase-split API: seed_batch → extend_batch → packed BAM records. align_batch is a thin wrapper = seed + extend. estimate_pestat runs seed + SE extension + mem_pestat only, skipping pairing and emission.

Re-exports

pub use align::align_batch;

pub use align::estimate_pestat;

pub use align::extend_batch;

pub use align::seed_batch;

pub use align::AlignmentBatch;

pub use align::ReadPair;

pub use align::Record;

pub use align::Seeds;

pub use error::Error;

pub use error::Result;

pub use index::BwaIndex;

pub use opts::MemOpts;

pub use opts::MemPeStat;

pub use opts::Mode;

pub use opts::PeOrient;

pub use opts::PeOrientation;

pub use xa::parse_xa;

pub use xa::AuxHit;

Modules

align

Read-pair input, seed/alignment batch handles, and the public align functions.

error

Error types for the bwa-mem2-rs crate.

index

Reference index handle.

opts

Alignment options and paired-end insert-size model.

xa

Parser for XA:Z: aux tags — bwa’s alt-hit encoding.