[theontho]

Document that the existing automatic short-read aligner selection also uses native BWA-MEM2 on Windows when its reference index is present and fits in memory. The Windows guide now shows how to prepare the index and explains the BWA fallback for smaller-memory machines.

Keep the BWA-MEM2 metadata fixtures small: the memory checks use lengths from the .fai, so the tests can model a human reference without writing gigabytes of dummy sequence. The separate real alignment test still creates and aligns actual sequence.

Validation:

• Installed native Windows BWA-MEM2 and the CLI --aligner auto pipeline produced decoded alignment records identical to Linux on matched real chromosome-region inputs.
• BWA-MEM2 tests: 12 passed; runtime fell from 52.31s to 3.26s.
• Ordinary local suite: 1,880 passed, 30 skipped, 87 deselected.
• Ruff, formatting, pre-commit, source mypy, and diff checks passed.

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🟢 Approval recommended

No active review issues remain for the Windows BWA-MEM2 documentation and metadata-only test changes.

No open issues 🎉

What changed in this PR

This PR documents existing native Windows BWA-MEM2 support in automatic short-read aligner selection and reduces the cost of metadata-only tests. It does not change runtime alignment behavior.

Changes:

• Adds Windows to the documented platforms supporting automatic BWA-MEM2 selection.
• Explains Windows index preparation, memory requirements, and fallback to BWA.
• Uses a tiny FASTA fixture while retaining simulated reference lengths in .fai metadata.

File	Description
tests/​test_bwa_mem2.py	Avoids writing large dummy sequences for metadata-only tests.
README.md	Includes Windows in the BWA-MEM2 platform documentation.
docs/​windows.md	Documents automatic selection, index preparation, and memory considerations.

_{Review effort: Balanced}