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Fix an instance of non-determinism in HaplotypeCaller #6104

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merged 3 commits into from
Aug 27, 2019
Merged

Fix an instance of non-determinism in HaplotypeCaller #6104

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4b01aec
Fix non-determinism in HaplotypeCaller
lbergelson Aug 20, 2019
75240b2
fix the tests by arbitrarily reversing the comparator, pull the compa…
lbergelson Aug 20, 2019
1319df2
Update src/main/java/org/broadinstitute/hellbender/tools/walkers/hapl…
lbergelson Aug 21, 2019
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7 changes: 5 additions & 2 deletions .../broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/KBestHaplotypeFinder.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs;

import org.apache.commons.lang3.mutable.MutableInt;
import org.broadinstitute.hellbender.utils.BaseUtils;
import org.broadinstitute.hellbender.utils.Utils;
import org.jgrapht.alg.CycleDetector;

Expand All @@ -14,6 +15,9 @@
*/
public final class KBestHaplotypeFinder {

public static final Comparator<KBestHaplotype> K_BEST_HAPLOTYPE_COMPARATOR = Comparator.comparingDouble(KBestHaplotype::score)
.reversed()
.thenComparing(KBestHaplotype::getBases, BaseUtils.BASES_COMPARATOR.reversed()); // This is an arbitrary deterministic tie breaker.
private final SeqGraph graph;
final Set<SeqVertex> sinks;
final Set<SeqVertex> sources;
Expand Down Expand Up @@ -66,7 +70,7 @@ public KBestHaplotypeFinder(final SeqGraph graph) {
*/
public List<KBestHaplotype> findBestHaplotypes(final int maxNumberOfHaplotypes) {
final List<KBestHaplotype> result = new ArrayList<>();
final PriorityQueue<KBestHaplotype> queue = new PriorityQueue<>(Comparator.comparingDouble(KBestHaplotype::score).reversed());
final PriorityQueue<KBestHaplotype> queue = new PriorityQueue<>(K_BEST_HAPLOTYPE_COMPARATOR);
sources.forEach(source -> queue.add(new KBestHaplotype(source, graph)));

final Map<SeqVertex, MutableInt> vertexCounts = graph.vertexSet().stream()
Expand All @@ -86,7 +90,6 @@ public List<KBestHaplotype> findBestHaplotypes(final int maxNumberOfHaplotypes)
}

for (final BaseEdge edge : outgoingEdges) {
final SeqVertex targetVertex = graph.getEdgeTarget(edge);
queue.add(new KBestHaplotype(pathToExtend, edge, totalOutgoingMultiplicity));
}
}
Expand Down