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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
C++ bug fixes:
- AlleleAges.cpp: fix infinite loops from self-ref in carrier chain
and trace path, add target<0 guard for out-of-bounds crash
- DataConsistency.cpp: fix infinite loop in carrier traversal, fix
silent mismatch skipping from self-ref targets (replaced with sample 0)
Optimizations:
- Vectorized emission probabilities in fwbw.py
- Optimized sparse posterior construction and VCF writing in impute.py
Tests:
- 152 new unit/property/integration tests covering infer, convert, map,
impute, vcf, normalization, and allele ages
- Benchmarks for imputation scaling and compression
Cleanup:
- Removed dead phase.py (broken imports, no CLI registration)
- allele_ages: remove unnecessary np.array() conversion in per-site loop,
replace multiprocessing.Manager().dict() with pool.imap() return values
- map: lazy-import ray (~1s startup saving when single-threaded),
remove per-variant time.time() instrumentation from hot loop
- convert: lazy-import tszip (~0.7s saving when writing .argn only),
skip guaranteed-fail noise=0.0 retry, narrow bare except to RuntimeError
- Add bulk C++ functions for estimate_ages and run_consistency,
eliminating per-site Python/C++ round-trips
- Replace click with argparse (saves ~224ms import time)
- Replace h5py with C++ HDF5 reader/writer (saves ~235ms import time)
- Move h5py from core to dev dependency
- Port forward/backward LS algorithm from numba to C++
- Add VariantMetadata lightweight class replacing pandas DataFrame
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Bug fixes:
Performance:
Testing: