fix(correctness): prevent arithmetic overflow, underflow panics, and …

[IgnatiusPang]

Pull Request: Fix boundary panics, integer overflow/underflow, and slice bounds in bitkmer, kmer, and sequence

Source Branch: fix/boundary-and-overflow-robustness
Target Repository: onecodex/needletail (master)
Commit: f417b8f (fix(correctness): prevent arithmetic overflow, underflow panics, and slice boundary issues)

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GitHub Pull Request Template

## Description

This PR resolves arithmetic overflow/underflow conditions, boundary panics, and slice indexing defects across `bitkmer`, `kmer`, and `sequence` in `needletail`:

1. **32-mer Exponentiation Overflow in `bitkmer::extend_kmer`**: `BitKmerSeq::pow(2, u32::from(2 * kmer.1)) - 1` was evaluated on `u64`. For standard 32-mer k-mers (`kmer.1 == 32`), `2 * kmer.1 == 64`, which panics in Rust with `attempt to calculate 2_u64.pow(64_u32), which would overflow` ($2^{64} > \text{u64::MAX}$). Replaced with `BitKmerSeq::MAX` for 32-mers, enabling safe 32-mer analysis.
2. **Underflow and Exponentiation Overflow in `bitkmer::minimizer`**: For 32-mer minimizers, `pow(2, 2 * minmer_size)` overflowed. Additionally, when `minmer_size > kmer.1`, `kmer.1 - minmer_size` underflowed `u8` in debug mode. Guarded with early return and clamped bitmask.
3. **Underflow and Shift Overflow in `bitkmer::bitmer_to_bytes`**: When `kmer.1 == 0`, `offset = (kmer.1 - 1) * 2` and `2 * kmer.1 - 1` underflowed `u8` to 255, resulting in panic on `2u64.pow(255)`. Handled 0-length k-mers returning an empty vector immediately, and guarded `kmer.1 == 32`.
4. **Unsigned Integer Underflow Panic in `kmer::CanonicalKmers`**: When initialized with `k == 0`, `(self.k - 1) as usize` evaluated `0u8 - 1`, panicking in debug mode with `attempt to subtract with overflow`. Added early return in `update_position`.
5. **Algorithmic Scan Stalling / Quadratic Re-scanning on Invalid Bases**: In `bitkmer::update_position` and `CanonicalKmers::update_position`, `kmer_len = 0;` was executed before advancing `start_pos += kmer_len + 1;`, causing `start_pos` to advance by only 1 base instead of advancing past the invalid base. Fixed position advancement order.
6. **Slice Out-of-Bounds Panic on Short Sequences in `sequence::minimizer`**: `&seq[..length]` was evaluated without validating sequence length, panicking with `range end out of range for slice` when `seq.len() < length`. Added early return `Cow::Borrowed(seq)` when `seq.len() < length`.

All changes include regression unit tests and pass all library and integration test suites.

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### Key Fixes

#### 1. `src/bitkmer.rs`: 32-mer Overflow & Zero-Length Underflow
- Masked bits with `BitKmerSeq::MAX` when `kmer.1 >= 32`.
- Advanced `*start_pos += kmer_len + 1` before resetting `kmer_len = 0`.
- Early return `(0, kmer.1)` in `minimizer` when `minmer_size == 0 || minmer_size > kmer.1`.
- Handled `kmer.1 == 0` in `bitmer_to_bytes`.
- Added tests: `test_32mer_support`, `test_zero_kmer_safety`, `test_minimizer_32mer`.

#### 2. `src/kmer.rs`: Zero-Length Guard in `CanonicalKmers`
- Added `if self.k == 0 { return false; }` in `CanonicalKmers::update_position`.
- Fixed `start_pos` advancement order on invalid characters.
- Added test: `test_canonical_kmers_zero_k`.

#### 3. `src/sequence.rs`: Short Sequence Guard in `minimizer`
- Returned `Cow::Borrowed(seq)` when `length == 0 || seq.len() < length`.
- Updated test: `can_minimize` to verify short and empty sequence inputs.

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## Validation

- `cargo test --lib`: 45 passed (0 failed)
- `cargo test --tests`: 53 passed (0 failed)
- `cargo fmt --check`: passed cleanly

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[audy]

Thanks. The k=32 overflow is real and I'll fix it separately. Closing because this bundles unrelated changes and conflicts with #121. In the future, please open an issue and disclose AI-generated contributions.