Implement eNRSA algorithmic optimizations for speed and memory

[edmundmiller]

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/