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DEVERLOPERGUIDE.md

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  • apples/PoolQuerkWorker.py: the main worker each thread runs
    • the function runquery is the entry point
    • One worker per thread
    • Each worker gets its private copy of all the data structure including reference
  • apples/reference.py: the reference tree, with all the preprocessing results included
    • build_appledb.py: builds an apple reference without any queries; it can be pickled.
  • FM.py, BE.py, etc.: the algorithm implementations.
    • Entry point is dp_frag.
    • placement_per_edge: computes the error for each edge
    • placement: finds the best edge
  • subtree.py: computes the subtree relevant per query for a given alignment.
    • validate_edges is the main function that decides what to ignore. This works based on obs-dist calculated before.
    • similar function in PoolQuerkWorker.py for when distances are given as input.
    • unroll_changes: removes changes before going to the next query