Fix #151: max_assembly_sequences circuit breaker#156
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When the number of variant sequences after substring collapse exceeds max_assembly_sequences (default 1000), skip the O(n^2)-per-round greedy merge and return sequences sorted by read support. This prevents silent hangs on high-coverage loci. Three new tests: breaker triggers above threshold, disabled with None, normal merge below threshold. Fixes #151
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coverage: 93.077% (+0.009%) from 93.068% — fix-151-max-sequences-circuit-breaker into master |
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Summary
max_assembly_sequencesparameter toiterative_overlap_assembly(default 1000).Fixes #151
Test plan
./test.shpasses (166 tests)./lint.shpasses