Simplified and sped KBestHaplotypeFinder by replacing recursion with …

…Dijkstra's algorithm
broadinstitute · Dec 27, 2018 · 2834e09 · 2834e09
1 parent b928029
commit 2834e09
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Showing 19 changed files with 113 additions and 1,626 deletions.
diff --git a/...g/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/AdaptiveChainPruner.java b/...g/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/AdaptiveChainPruner.java
@@ -51,7 +51,7 @@ private Collection<Path<V,E>> likelyErrorChains(final List<Path<V, E>> chains, f
 
         chains.stream().filter(c -> isChainPossibleVariant(c, graph))
                 .sorted(Comparator.comparingDouble((ToDoubleFunction<Path<V, E>>) chainLogOdds::get)
-                        .reversed().thenComparingInt(Path::getScore))
+                        .reversed().thenComparingInt(Path::length))
                 .skip(maxUnprunedVariants)
                 .forEach(result::add);
 

diff --git a/...stitute/hellbender/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java b/...stitute/hellbender/tools/walkers/haplotypecaller/graphs/AggregatedSubHaplotypeFinder.java
diff --git a/...itute/hellbender/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java b/...itute/hellbender/tools/walkers/haplotypecaller/graphs/DeadEndKBestSubHaplotypeFinder.java