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Searched refs:getBasesForPath (Results 1 – 3 of 3) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/
H A DAbstractReadThreadingGraph.java680 final byte[] refBases = getBasesForPath(refPath, false); in generateCigarAgainstDownwardsReferencePath()
681 final byte[] altBases = getBasesForPath(altPath, false); in generateCigarAgainstDownwardsReferencePath()
712 final byte[] refBases = getBasesForPath(refPath, true); in generateCigarAgainstUpwardsReferencePath()
713 final byte[] altBases = getBasesForPath(altPath, true); in generateCigarAgainstUpwardsReferencePath()
845 byte[] getBasesForPath(final List<MultiDeBruijnVertex> path, final boolean expandSource) { in getBasesForPath() method in AbstractReadThreadingGraph
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/readthreading/
H A DReadThreadingGraphUnitTest.java469 final String resultForTails = new String(graph.getBasesForPath(vertexes, false)); in testGetBasesForPath()
471 final String resultForHeads = new String(graph.getBasesForPath(vertexes, true)); in testGetBasesForPath()
H A DJunctionTreeLinkedDeBruijnGraphUnitTest.java986 final String resultForTails = new String(graph.getBasesForPath(vertexes, false)); in testGetBasesForPath()
988 final String resultForHeads = new String(graph.getBasesForPath(vertexes, true)); in testGetBasesForPath()