Roadmap

Current version: v0.1.0 — Single-end BWA-MEM style aligner, all planned tasks completed.

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Project Goals

Implement a Rust aligner inspired by BWA:

• Architecture and algorithms follow BWA/BWA-MEM
• Not aiming for 100% behavioral compatibility
• Prioritize correctness, readability, and memory safety

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v0.1.0 ✅ Completed

Phase	Content	Status
Baseline	Goal definition, test datasets, dev scripts	✅
Index	FASTA parsing, FM index serialization, SA/BWT verification	✅
Alignment MVP	Config, seed + banded SW, CIGAR/NM output	✅
BWA-MEM Style	SMEM seeds, chaining, extension, MAPQ	✅
Performance	Benchmarks, multi-threading, sparse SA, buffer reuse	✅
Docs	Architecture docs, tutorial, examples, CI	✅

Post-v0.1.0 Improvements

Improvement	Description	Status
Memory protection	max_occ, max_chains, max_alignments	✅
Alignment quality	Semi-global refinement, clip penalty ranking	✅
Input validation	FASTA error detection, parameter validation	✅
Code quality	Named constants, API doc comments	✅

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Future Plans

Version	Milestone	Key Features
v0.2.0	Paired-end	PE reads, insert size estimation, mate rescue
v0.3.0	Index compat	Read BWA native index files
v0.4.0	Output	Direct BAM output, sorted output
v0.5.0	Performance	SIMD acceleration, mmap index
v1.0.0	Production	Human genome validation, stable API

See docs/plan.md for detailed design.

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Versioning

This project follows Semantic Versioning: MAJOR.MINOR.PATCH

Part	Meaning
MAJOR	Breaking changes (API, index format)
MINOR	New features, backward compatible
PATCH	Bug fixes, performance tweaks

0.x Phase Rules

• API and index format allow breaking changes
• Breaking changes marked BREAKING in CHANGELOG
• .fm index version field used for compatibility checks

Conditions for 1.0.0

1. ✅ Human genome (hg38) level correctness validation passes
2. ✅ Mapping rate within reasonable range vs C BWA
3. ✅ Public API stable
4. ✅ Documentation and error handling reach production quality

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Index Format Version

Version	Change
v1	Initial format
v2	Added IndexMeta build metadata

• Software upgrades without index format changes → no rebuild needed
• Breaking index format changes → increment version, error on load

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Release Process

# Code quality checks
cargo fmt --all -- --check
cargo clippy --all-targets --all-features -- -D warnings
cargo test --all-targets --all-features

# Release build
cargo build --release

# Create tag
git tag v0.x.x
git push origin v0.x.x

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Test Coverage

Type	Count
Unit tests	151
Integration tests	11
Module tests	5
Doc tests	1
Total	168

CI Pipeline: GitHub Actions (fmt → clippy → test → release)