Add counts_only aggregate mode#26
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New Matcher(counts_only=True) returns per (query peptide, mismatch level) hit counts instead of the full per-hit table. The Rust count path mirrors mismatch_match's dedup + validity walk exactly but tallies per mismatch level without reconstructing matched sequences, pulling metadata, or building rows -- so memory is O(unique queries), not O(hits), i.e. density-proof, and it skips the per-hit work. Schema: [Query ID, Query Sequence, Mismatches, Count]; honors output_format. Rejected with best_match; linear search only. Parity test asserts counts == full output grouped by (peptide, mismatch level). Dense bench: 1106MB/11.8s (full) -> 235MB/8.9s (counts), result rows bounded by unique peptides regardless of hit count.
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New Matcher(counts_only=True) returns per (query peptide, mismatch level) hit counts instead of the full per-hit table. The Rust count path mirrors mismatch_match's dedup + validity walk exactly but tallies per mismatch level without reconstructing matched sequences, pulling metadata, or building rows, so memory is O(unique queries), not O(hits) and it skips the per-hit work. Schema: [Query ID, Query Sequence, Mismatches, Count]; honors output_format. Rejected with best_match; linear search only.
Parity test asserts counts == full output grouped by (peptide, mismatch level). Dense bench: 1106MB/11.8s (full) -> 235MB/8.9s (counts), result rows bounded by unique peptides regardless of hit count.