Put chromosomes in MRCA routines

[hyanwong]

All algorithms should now be chromosome-aware

Summary by CodeRabbit

• New Features

  • Enhanced genetic inheritance graph library with methods for better edge and chromosome-specific analysis.
  • Added functionality to find regions between nodes with optional chromosome restrictions.

• Bug Fixes

  • Improved handling of chromosome specifics in various methods to ensure accurate genetic simulations.

• Tests

  • Updated test cases to align with new features and changes in handling chromosome-specific data.
  • Modified assertions in tests to include new chromosome parameters and verify the correctness of genetic regions.

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Commits

Files that changed from the base of the PR and between 67df44ea9638a27a9b3473b6958fcce72967ba54 and 59a0fe5fb6d191a52551173d25989892e902b271.

Walkthrough

The update refines MRCA routines and introduces chromosome-specific methods in the GeneticInheritanceGraphLibrary, enhancing genetic inheritance simulations' precision and functionality.

Changes

File Path	Change Summary
.../tables.py, GeneticInheritanceGraphLibrary/graph.py	Added methods for MRCA handling, improved efficiency in sample_resolve, and updated chromosome-specific operations.
tests/gigutil.py, tests/test_gigutil.py	Adjusted methods for new parameter orders, chromosome-specific processing, and inclusion of chromosome information in tests.
tests/test_tables.py	Enhanced test assertions, introduced chromosome-specific checks, and updated method behaviors for better testing.

Possibly related issues

• Issue #112: Adjust MRCA routines to account for different chromosomes. The changes in find_mrca_regions to handle chromosome restrictions directly address this issue.
• Issue #78: Develop visualization tools for MRCA structure. The enhancements in MRCA-related methods could facilitate the visualization tools discussed in this issue.

Poem

🐰 Oh hop and leap, the code does change,
🌟 With tweaks and twists, it rearranges.
🧬 For genes that weave through time and space,
📊 A graph that charts each chromosomal trace.
🎉 Celebrate each line, each clause,
🚀 For in our code, we find no pause!

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