Implement eNRSA algorithmic optimizations for speed and memory

## Summary Integrate eNRSA's performance optimizations including binned processing and single-pass algorithms. ## Features to implement - 200bp binning for count matrix generation - Chromosome-specific processing - Single-pass count matrix generation - Memory-efficient data structures ## Implementation details - Rewrite count matrix generation with binning approach - Implement chromosome-level parallelization - Add precomputed data storage optimization - Create memory-efficient processing modules ## Expected performance gains - 20x faster execution - 8x reduced memory usage - Better scalability for large datasets ## Acceptance criteria - [ ] Binned processing implementation - [ ] Chromosome-specific parallelization - [ ] Significant performance improvements verified - [ ] Memory usage reduction confirmed - [ ] Maintained output accuracy ## References - eNRSA performance optimizations: https://bioinfo.vanderbilt.edu/eNRSA/