Package org.broadinstitute.gatk.utils.collections

Examples of org.broadinstitute.gatk.utils.collections.CountSet$MyIterator

580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
        final Set<ReadSegmentCost> readSegmentCosts = new TreeSet<>(ReadSegmentComparator.INSTANCE);

        final int readStart = beforeBlockReadOffset + kmerSize;
        final int readEnd = Math.max(readStart, afterBlockReadOffset + kmerSize - 1);
        final byte[][] pathBases = new byte[acrossBlockPaths.size()][];
        final CountSet pathSizes = new CountSet(acrossBlockPaths.size());
        int nextPath = 0;

        // Complete the read segment cost with the corresponding path bases
        for (final Route<MultiDeBruijnVertex, MultiSampleEdge> p : acrossBlockPaths) {
            final ReadSegmentCost readSegmentCost = new ReadSegmentCost(read, p, 0);
            pathBases[nextPath++] = readSegmentCost.bases = eventBlockPathBases(p, includePathEnds);
            pathSizes.add(readSegmentCost.bases.length);
            readSegmentCosts.add(readSegmentCost);
        }

        // Add the read 'path size'.
        pathSizes.add(readEnd - readStart);

        final byte[] readBases = hmm.getReadBases();

        // Perform right clipping of bases that are common to all paths and read.
        int rightClipping = !doClipping ? 0 : calculateRightClipping(readEnd, pathBases, readBases,pathSizes);
View Full Code Here
100
101
102
103
104
105
106
     */
    public AssemblyResultSet() {
        assemblyResultByKmerSize = new LinkedHashMap<>(4);
        haplotypes = new LinkedHashSet<>(10);
        assemblyResultByHaplotype = new LinkedHashMap<>(10);
        kmerSizes = new CountSet(4);
    }
View Full Code Here
902
903
904
905
906
907
908
909
910
911
912
913
        int index = currentVertex.getSequence().length - 1;
        nonAnchorableDueToRepeats[index] = !sourceIsAnchorable;


        // We keep record on all alternative path lengths:
        final CountSet pathLengths = new CountSet(haplotypes.size());
        pathLengths.setTo(0);

        // Now we go through the reference path and determine which vertices are not part of event block.
        // We keep track of open divergent paths in expectedRejoins. Thus only those vertices traversed
        // when exptectedRejoins size 0 can be anchorable:
        while (currentVertex != null) {
View Full Code Here
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
        depths.add(prefixSizes);

        final Set<MultiDeBruijnVertex> visited = new HashSet<>();
        if (!exhaustive) visited.add(startVertex);
        while (!queue.isEmpty()) {
            final CountSet depth = depths.remove();
            final MultiDeBruijnVertex v = queue.remove();
            if (referenceVertices.contains(v)) {
                if (referenceWithinBoundaries.contains(v)) {
                    final CountSet previous = expectedRejoins.get(v);
                    if (previous == null)
                        expectedRejoins.put(v, depth.clone());
                    else
                        previous.addAll(depth);
                }
            } else {
                final CountSet depthPlusOne = depth.clone();
                depthPlusOne.incAll(1);
                final Set<MultiSampleEdge> nextEdges = backwards ? incomingEdgesOf(v) : outgoingEdgesOf(v);
                for (final MultiSampleEdge e : nextEdges) {
                    final MultiDeBruijnVertex w = backwards ? getEdgeSource(e) : getEdgeTarget(e);
                    if (visited.contains(w)) // avoid repetitive work.
                        continue;
View Full Code Here
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
            final ReadAnchoring anchoring, final boolean backwards,
            final MultiDeBruijnVertex leftVertex, final MultiDeBruijnVertex rightVertex) {

        MultiDeBruijnVertex currentVertex = backwards ? rightVertex : leftVertex;
        boolean foundEvent = false;
        final CountSet pathSizes = new CountSet(10); // typically more than enough.
        pathSizes.setTo(0);

        // Map between reference vertices where there is some expected open alternative path rejoining and the
        // predicted length of paths rejoining at that point counting from the beginning of the block.
        final Map<MultiDeBruijnVertex, CountSet> expectedAlternativePathRejoins = new HashMap<>(4);

        // Keeps record of possible left-clipping veritces; those that are located before any event path furcation
        // has been found. The value indicates the blockLength at the time we traverse that node.
        final Deque<Pair<MultiDeBruijnVertex, Integer>> possibleClippingPoints = new LinkedList<>();

        // We keep the distance from the beggining of the block (leftVertex).
        int blockLength = 0;
        while (currentVertex != null) {
            int openingDegree = backwards ? graph.outDegreeOf(currentVertex) : graph.inDegreeOf(currentVertex);
            if (openingDegree > 1) {
                final CountSet joiningPathLengths = expectedAlternativePathRejoins.remove(currentVertex);
                if (joiningPathLengths != null)
                    pathSizes.addAll(joiningPathLengths);
            }
            final boolean isValidBlockEnd = isValidBlockEnd(anchoring, currentVertex, expectedAlternativePathRejoins);
            if (foundEvent && isValidBlockEnd) // !gotcha we found a valid block end.
View Full Code Here
266
267
268
269
270
271
272
273
274
275
276
277
        for (final MultiSampleEdge e : nextEdges) {
            final MultiDeBruijnVertex nextVertex = backwards ? graph.getEdgeSource(e) : graph.getEdgeTarget(e);
            if (e.isRef())
                nextReferenceVertex = nextVertex;
            else {
                final CountSet pathSizesPlusOne = pathSizes.clone();
                pathSizesPlusOne.incAll(1);
                graph.calculateRejoins(nextVertex, expectedAlternativePathRejoins, anchoring.referenceWithinAnchorsMap.keySet(), pathSizesPlusOne, true, backwards);
            }
        }
        return nextReferenceVertex;
    }
View Full Code Here
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
            final ReadAnchoring anchoring, final boolean backwards,
            final MultiDeBruijnVertex leftVertex, final MultiDeBruijnVertex rightVertex) {

        MultiDeBruijnVertex currentVertex = backwards ? rightVertex : leftVertex;
        boolean foundEvent = false;
        final CountSet pathSizes = new CountSet(10); // typically more than enough.
        pathSizes.setTo(0);

        // Map between reference vertices where there is some expected open alternative path rejoining and the
        // predicted length of paths rejoining at that point counting from the beginning of the block.
        final Map<MultiDeBruijnVertex, CountSet> expectedAlternativePathRejoins = new HashMap<>(4);

        // Keeps record of possible left-clipping veritces; those that are located before any event path furcation
        // has been found. The value indicates the blockLength at the time we traverse that node.
        final Deque<Pair<MultiDeBruijnVertex, Integer>> possibleClippingPoints = new LinkedList<>();

        // We keep the distance from the beggining of the block (leftVertex).
        int blockLength = 0;
        while (currentVertex != null) {
            int openingDegree = backwards ? graph.outDegreeOf(currentVertex) : graph.inDegreeOf(currentVertex);
            if (openingDegree > 1) {
                final CountSet joiningPathLengths = expectedAlternativePathRejoins.remove(currentVertex);
                if (joiningPathLengths != null)
                    pathSizes.addAll(joiningPathLengths);
            }
            final boolean isValidBlockEnd = isValidBlockEnd(anchoring, currentVertex, expectedAlternativePathRejoins);
            if (foundEvent && isValidBlockEnd) // !gotcha we found a valid block end.
View Full Code Here
266
267
268
269
270
271
272
273
274
275
276
277
        for (final MultiSampleEdge e : nextEdges) {
            final MultiDeBruijnVertex nextVertex = backwards ? graph.getEdgeSource(e) : graph.getEdgeTarget(e);
            if (e.isRef())
                nextReferenceVertex = nextVertex;
            else {
                final CountSet pathSizesPlusOne = pathSizes.clone();
                pathSizesPlusOne.incAll(1);
                graph.calculateRejoins(nextVertex, expectedAlternativePathRejoins, anchoring.referenceWithinAnchorsMap.keySet(), pathSizesPlusOne, true, backwards);
            }
        }
        return nextReferenceVertex;
    }
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.utils.collections.CountSet$MyIterator

  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.EventBlockFinder
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.GraphBasedLikelihoodCalculationEngineInstance
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph
  • org.jgroups.Address
  • java.io.FileReader
  • java.io.BufferedReader
  • java.io.FileInputStream
  • java.util.zip.ZipInputStream
  • java.util.NoSuchElementException
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.