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This commit cleans up the repository by removing 183 temporary/debug files from the root directory and completely refreshing the README to accurately reflect SeqRush's current functionality. Changes: Root Directory Cleanup: - Removed temporary test data files (.fa, .fai, .paf, .odgi, .html, etc.) - Removed debug scripts and analysis tools (Python, shell scripts) - Removed development notes and historical documentation - Removed compiled artifacts and temp directories - Removed pafcheck submodule (no longer used) - Kept only essential files: source code, submodules, config files README Refresh: - Updated description to reflect actual implemented features - Removed "Planned" markers for completed features: * AllWave and SweepGA aligners (implemented) * Bidirected union-find (implemented) * Graph layout pipeline (implemented) * Iterative alignment (implemented) - Added comprehensive usage examples for all features - Documented iterative alignment with two-phase processing - Added sparsification strategies documentation - Included validation results from HLA-Zoo testing - Updated project structure to match actual codebase - Corrected repository URL to pangenome organization - Updated acknowledgments to reflect actual dependencies The repository now presents a clean, professional interface that accurately documents the tool's capabilities. All tests pass. Build verified.
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Summary
This PR cleans up the repository by removing 183 temporary/debug files from the root directory and completely refreshing the README to accurately reflect SeqRush's current functionality.
Changes
Root Directory Cleanup (183 files removed)
Files remaining in root (12 essential files):
README Complete Refresh
Old: "Prototype with Planned features"
New: Production tool with implemented features
Key updates:
Verification
cargo build --release --features use-allwavecargo test(100% pass rate)Impact
The repository now has a clean, professional presentation that accurately reflects SeqRush's actual capabilities. No functional changes.