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bugfix in wt counting, general improvements - #16
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Pass 2 (expected-library reconciliation) dominated runtime: pybktree's pure-Python tree walk dispatched the numba hamming ~1275x per query. Flatten the tree to CSR arrays and run the whole search in one numba nopython kernel (4.4x on pass 2, output bit-identical). Add a loud startup log of numba JIT status. Ship the ~137MB FastqToCounts to pool workers once via initializer instead of on every submit. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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counts_to_lncfuthat was improperly parsing genotypes and miscounting wildtype. This is now fixed.run_comparecode to be general rather than run-type specifictfs-process-fastqto be much fastertfs-configure-runnow does parameter number estimates and reports them prior to the run