Revert label propagation: restore DisjointSetsAsm for correctness#137
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Revert label propagation: restore DisjointSetsAsm for correctness#137
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The Shiloach-Vishkin label propagation had a race condition where parent[max(la,lb)] = min(la,lb) could link unrelated positions when la/lb were stale. This caused base mismatches in write_graph_chunk on larger inputs (e.g., USP14 region with 527 sequences, 212kb). Revert to DisjointSetsAsm (lock-free CAS-based union-find) which is proven correct. Keep all other optimizations: spanning tree BFS, orphan recovery, per-sequence iitree queries, adjacency list. MHC (466 seqs): 4m12s, correct (2727 nodes, 52047bp) USP14 (527 seqs): 19m60s, correct (10199 nodes, 236011bp) — was crashing
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Summary
The Shiloach-Vishkin label propagation introduced in PR #135 has a race condition that causes incorrect equivalence classes on larger inputs. Specifically,
parent[max(la,lb)] = min(la,lb)with Relaxed ordering can link unrelated positions whenla/lbare stale, causing base mismatches inwrite_graph_chunk.This reverts to
DisjointSetsAsm(lock-free CAS-based union-find) for correctness while keeping all other optimizations from #135:The bug
Reproduced on USP14 region (chr18:68526-280967, 527 sequences, 212kb).
Test results