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Fixed a rare non-determinism in the AdaptiveChainPruner #7851

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May 19, 2022
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Fixed a rare non-determinism in the AdaptiveChainPruner #7851

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3 changes: 2 additions & 1 deletion ...g/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/AdaptiveChainPruner.java
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,8 @@ private Collection<Path<V,E>> likelyErrorChains(final List<Path<V, E>> chains, f
// Note that chains can we added twice to the queue, once for each side
final PriorityQueue<Pair<Path<V,E>, Double>> chainsToAdd = new PriorityQueue<>(
Comparator.comparingDouble((Pair<Path<V,E>, Double> p) -> -p.getRight())
.thenComparing((Pair<Path<V,E>, Double> p) -> p.getLeft().getFirstVertex().getSequence(), BaseUtils.BASES_COMPARATOR));
.thenComparing((Pair<Path<V,E>, Double> p) -> p.getLeft().getFirstVertex().getSequence(), BaseUtils.BASES_COMPARATOR)
.thenComparing((Pair<Path<V,E>, Double> p) -> p.getLeft().getBases(), BaseUtils.BASES_COMPARATOR)); // Handle rare edge case for non-determinism where two chains with equivalent score start on the same vertex

// seed the subgraph of good chains by starting with some definitely-good chains. These include the max-weight chain
// and chains emanating from vertices with two incoming or two outgoing chains (plus one outgoing or incoming for a total of 3 or more) with good log odds
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