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91
...itute/hellbender/tools/walkers/haplotypecaller/graphs/GraphBasedKBestHaplotypeFinder.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| package org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs; | ||
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| import org.apache.commons.lang3.mutable.MutableInt; | ||
| import org.broadinstitute.hellbender.utils.BaseUtils; | ||
| import org.broadinstitute.hellbender.utils.Utils; | ||
| import org.jgrapht.alg.CycleDetector; | ||
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| import java.util.*; | ||
| import java.util.stream.Collectors; | ||
|
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| /** | ||
| * Efficient algorithm to obtain the list of best haplotypes given the {@link BaseGraph instance}. | ||
| * | ||
| * @author Valentin Ruano-Rubio <valentin@broadinstitute.org> | ||
| */ | ||
| public class GraphBasedKBestHaplotypeFinder<V extends BaseVertex, E extends BaseEdge> extends KBestHaplotypeFinder<V, E> { | ||
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| public final Comparator<KBestHaplotype<V, E>> K_BEST_HAPLOTYPE_COMPARATOR = Comparator.comparingDouble(KBestHaplotype<V, E>::score) | ||
| .reversed() | ||
| .thenComparing(KBestHaplotype<V, E>::getBases, BaseUtils.BASES_COMPARATOR.reversed()); // This is an arbitrary deterministic tie breaker. | ||
|
|
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| /** | ||
| * Constructs a new best haplotypes finder. | ||
| * | ||
| * @param graph the graph to search. | ||
| * @param sources source vertices for all haplotypes. | ||
| * @param sinks sink vertices for all haplotypes. | ||
| * | ||
| * @throws IllegalArgumentException if <ul> | ||
| * <li>any of {@code graph}, {@code sources} or {@code sinks} is {@code null} or</li> | ||
| * <li>any of {@code sources}' or any {@code sinks}' member is not a vertex in {@code graph}.</li> | ||
| * </ul> | ||
| */ | ||
| public GraphBasedKBestHaplotypeFinder(final BaseGraph<V, E> graph, final Set<V> sources, final Set<V> sinks) { | ||
| super(sinks, sources, graph); | ||
| } | ||
|
|
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| /** | ||
| * Constructor for the special case of a single source and sink | ||
| */ | ||
| public GraphBasedKBestHaplotypeFinder(final BaseGraph<V, E> graph, final V source, final V sink) { | ||
| this(graph, Collections.singleton(source), Collections.singleton(sink)); | ||
| } | ||
|
|
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| /** | ||
| * Constructor for the default case of all sources and sinks | ||
| */ | ||
| public GraphBasedKBestHaplotypeFinder(final BaseGraph<V, E> graph) { | ||
| this(graph, graph.getSources(), graph.getSinks()); | ||
| } | ||
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| @Override | ||
| public boolean keepCycles() { | ||
| return false; | ||
| } | ||
|
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| /** | ||
| * Implement Dijkstra's algorithm as described in https://en.wikipedia.org/wiki/K_shortest_path_routing | ||
| */ | ||
| @Override | ||
| public List<KBestHaplotype<V, E>> findBestHaplotypes(final int maxNumberOfHaplotypes) { | ||
| final List<KBestHaplotype<V, E>> result = new ArrayList<>(); | ||
| final PriorityQueue<KBestHaplotype<V, E>> queue = new PriorityQueue<>(K_BEST_HAPLOTYPE_COMPARATOR); | ||
| sources.forEach(source -> queue.add(new KBestHaplotype<>(source, graph))); | ||
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| final Map<V, MutableInt> vertexCounts = graph.vertexSet().stream() | ||
| .collect(Collectors.toMap(v -> v, v -> new MutableInt(0))); | ||
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| while (!queue.isEmpty() && result.size() < maxNumberOfHaplotypes) { | ||
| final KBestHaplotype<V, E> pathToExtend = queue.poll(); | ||
| final V vertexToExtend = pathToExtend.getLastVertex(); | ||
| if (sinks.contains(vertexToExtend)) { | ||
| result.add(pathToExtend); | ||
| } else { | ||
| if (vertexCounts.get(vertexToExtend).getAndIncrement() < maxNumberOfHaplotypes) { | ||
| final Set<E> outgoingEdges = graph.outgoingEdgesOf(vertexToExtend); | ||
| int totalOutgoingMultiplicity = 0; | ||
| for (final BaseEdge edge : outgoingEdges) { | ||
| totalOutgoingMultiplicity += edge.getMultiplicity(); | ||
| } | ||
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| for (final E edge : outgoingEdges) { | ||
| queue.add(new KBestHaplotype<>(pathToExtend, edge, totalOutgoingMultiplicity)); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| return result; | ||
| } | ||
|
|
||
| } |
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