Optimize inference#128
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ArniFreyrG wants to merge 9 commits into
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Bug fixes: - Fix incorrect error message in ThreadsLowMem constructor - Replace 20x exit(1) with throw for proper exception handling - Fix memory leak: raw HMM* → unique_ptr - Fix sign-extension in pair_key (int → uint32_t cast) - Fix sign bug in rho computation (visible at scale) Performance: - Replace unordered_map traceback storage with std::deque arena - Replace std::set neighbor search with boolean array scan in Matcher - Add periodic pruning every 500 sites (bounds memory, improves cache) - Replace hash maps with flat vectors in ThreadsLowMem/ViterbiState - Add NumPy batch API for Matcher, Viterbi, and hets phases - Use const int* in process_site to avoid bounds-check overhead - Improve move semantics and reference passing Testing: - Add 69 C++ unit tests (444 assertions) via Catch2
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This includes a subset of things from #127 geared towards optimizing inference only