fix: prevent integer overflow in band area calculation#1752
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ivan-aksamentov merged 6 commits intomasterfrom Feb 27, 2026
Merged
fix: prevent integer overflow in band area calculation#1752ivan-aksamentov merged 6 commits intomasterfrom
ivan-aksamentov merged 6 commits intomasterfrom
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Band area calculation in `regularize_stripes()` accumulates stripe widths across all reference positions (~R × W). For pathological inputs like concatenated genomes (179kb query vs 30kb reference), this yields ~3.6 billion, exceeding `u32::MAX` and causing overflow on 32-bit WASM. Debug builds panic with "attempt to add with overflow" before the `align.rs:80` guard can reject it with a proper error message. - Use `saturating_add()` to cap at `usize::MAX` (~4.3B), which still exceeds `max_band_area` (500M) so the downstream check correctly rejects with informative message - Reproducer: GISAID sequence EPI_ISL_20374993 (6 concatenated SARS-CoV-2 genomes) Fixes: #1749
Defense-in-depth fix for `calculate_dimensions()` which has the same accumulation pattern as `seed_alignment.rs` (fixed in 9d95d0a). In normal operation this is protected by the band_area check in `align.rs:80`, but could be reached through future code changes, direct `Band2d::new()` calls, or edge cases with many narrow stripes. - Use `saturating_add()` for consistency; overflow causes OOM on allocation rather than silent memory corruption via wrapped indices Ref: #1749
Band area calculation accumulates stripe widths across all reference positions (R × W). For pathological inputs like concatenated genomes (e.g., 179kb query vs 30kb reference), this yields ~3.7 billion, which exceeds `u32::MAX` (~4.3B) and causes overflow on 32-bit WASM. Previous fix (9d95d0a) used `saturating_add()` to prevent panic, but saturated values produce misleading error messages. Using `u64` ensures accurate calculation on both 32-bit (WASM) and 64-bit platforms without saturation artifacts. - Change `max_band_area` parameter from `usize` to `u64` - Change `create_alignment_band()` return type from `(Vec<Stripe>, usize)` to `(Vec<Stripe>, u64)` - Accumulate band area as `u64` in `regularize_stripes()` - Update JSON schemas to reflect `uint64` format Ref: #1749
The previous error message ("Alignment matrix size X exceeds maximum value Y") was uninformative for non-technical users who don't understand banded Smith-Waterman alignment.
The new message:
- Formats large numbers for readability (3.7B instead of 3704350009, 179,151 instead of 179151)
- States observable facts: query and reference sequence lengths
- Differentiates between two failure modes based on length ratio:
- Query >1.5× reference: likely concatenated sequences or assembly scaffolds
- Similar lengths: likely structural rearrangements or wrong reference
- Lists possible causes as hypotheses, not assertions
- Preserves technical details for advanced users
Example output:
```
Alignment band area (3.7B) exceeds limit (500M). Query sequence length (179,151 nt) is significantly larger than reference (29,903 nt). Possible reasons: concatenated sequences, assembly scaffolds, or wrong reference sequence.
```
Ref: #1749
Add configurable HumanFormat with builder pattern supporting: - Grouping styles (Standard, Indian, None) - Custom separator character - Compact notation (K/M/B/T suffixes) - Configurable threshold and decimal places
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Band area calculations could overflow on 32-bit WASM when aligning very long sequences against highly divergent references. This PR uses u64 for intermediate calculations and provides actionable error messages with human-readable numbers when the band area limit is exceeded.
format_number_humanutility for reuse