implement CoverageTrack with RLE compression for #62#99
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Comprehensive test suite for CoverageTrack RLE compression with quantization: Unit tests (14): - Uniform coverage (single run) - Alternating coverage (many runs) - Zero coverage regions - Quantization to nearest 5 (exact multiples, boundaries, rounding) - Random access via binary search (O(log n)) - Out-of-bounds access - Iterator over positions - Empty coverage edge case - Single position edge case - Realistic bacterial genome (4.6Mbp with variation) - High depth sequencing (100x) - Serialization round-trip Property tests (5): - Round-trip encode/decode equality (modulo quantization) - Quantization idempotence (quantize twice == quantize once) - coverage_at(i) matches to_vec()[i] - All decompressed values are multiples of 5 - Quantized values within ±2 of original Benchmarks: - Compression ratio on uniform, realistic, high-variation, and random coverage - Random access performance via binary search - Full decompression performance All tests FAIL as expected (RED phase) - implementation deferred to separate agent. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Implement run-length encoding (RLE) compression for CoverageTrack with: - Quantization to nearest 5 (e.g., 7 → 5, 13 → 15) - RLE encoding: compress runs of identical quantized values as (value, length) pairs - RLE decoding: decompress to full coverage array for validation - Random access: coverage_at(pos) returns value via binary search in O(log runs) time - Construction from Vec<usize> (coverage per position) - Iterator over (position, coverage) for decompression All 46 tests pass: - 14 unit tests covering uniform/alternating/zero-coverage/realistic scenarios - 5 property tests covering round-trip encode/decode, quantization idempotence, etc. - Quantization boundary tests (handles 2→0, 3→5, 7→5, 8→10 correctly) - Serialization via serde (Serialize/Deserialize traits) - Random access and iterator correctness Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
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Closing stale PR. Work has been superseded or merged via alternative approach. |
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Summary
Implement run-length encoding (RLE) compression for CoverageTrack in phraya-core. Coverage values are quantized to the nearest 5 before encoding to reduce storage overhead while preserving precision for biological applications.
Key Features
coverage_at(pos).phrayafile formatTest Coverage
Acceptance Criteria Met
Test Plan
cargo test -p phraya-core typesto validate all 46 tests passcargo test -p phraya-core coverage_track --libto focus on 14 CoverageTrack testscargo test -p phraya-core property_ --libto validate 5 property testscargo clippy -p phraya-coreto ensure no linting issuescargo fmt -p phraya-core -- --checkto verify formattingGenerated with Claude Code