v0.1.7 - Memory Optimization Release

v0.1.7 - Memory Optimization Release

This release brings significant memory and performance optimizations to discoal while maintaining 100% backward compatibility. This serves as a transitional release before the upcoming tskit integration.

Highlights

• 80-99% memory reduction for most simulation scenarios
• Up to 50x performance improvement for high mutation rates
• Sample size limit increased from 254 to 65,535

Major Improvements

Memory Optimizations

• Dynamic allocation replaces fixed-size arrays (baseline memory: 400MB → 10MB)
• Ancestry tracking via interval trees instead of per-site arrays
• Memory-mapped files for sweep trajectories (2GB → 1.4MB)
• Reference counting enables memory sharing between nodes
• Active material tracking with segment-based structure

Performance Enhancements

• Optimized mutation handling with hash tables and binary search
• Pre-computed mutation presence matrix for output generation
• AVL tree indexing for O(log n) ancestry lookups
• Up to 50x speedup for extreme mutation rates (θ=10,000)
• 33-47x faster for extreme recombination scenarios

# Same command-line interface as v0.1.6
./discoal 50 1000 10000 -t 10 -r 10

Installation

git clone https://github.com/kr-colab/discoal.git
cd discoal
make discoal

What's Next?

The next major release (v0.2.0) will introduce full tskit integration for tree sequence recording, bringing discoal into the modern tree sequence ecosystem.