Cleanup, unit test, and optimize KBestPaths and Path
-- Split Path from inner class of KBestPaths -- Use google MinMaxPriorityQueue to track best k paths, a more efficient implementation -- Path now properly typed throughout the code -- Path maintains a on-demand hashset of BaseEdges so that path.containsEdge is fast
This commit is contained in:
Mark DePristo
parent
98c4cd060d
commit
1fa5050faf
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@ -325,7 +325,7 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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}
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for( final SeqGraph graph : graphs ) {
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for ( final KBestPaths.Path path : new KBestPaths<SeqVertex>().getKBestPaths(graph, NUM_BEST_PATHS_PER_KMER_GRAPH) ) {
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for ( final Path<SeqVertex> path : new KBestPaths<SeqVertex>().getKBestPaths(graph, NUM_BEST_PATHS_PER_KMER_GRAPH) ) {
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Haplotype h = new Haplotype( path.getBases() );
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if( !returnHaplotypes.contains(h) ) {
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final Cigar cigar = path.calculateCigar();
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@ -46,293 +46,44 @@
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package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
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import com.google.common.collect.MinMaxPriorityQueue;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import net.sf.samtools.Cigar;
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import net.sf.samtools.CigarElement;
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import net.sf.samtools.CigarOperator;
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import org.apache.commons.lang.ArrayUtils;
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import org.broadinstitute.sting.utils.SWPairwiseAlignment;
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import org.broadinstitute.sting.utils.sam.AlignmentUtils;
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import java.io.Serializable;
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import java.util.*;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.List;
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/**
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* Created by IntelliJ IDEA.
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* User: ebanks, rpoplin
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* Class for finding the K best paths (as determined by the sum of multiplicities of the edges) in a graph.
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* This is different from most graph traversals because we want to test paths from any source node to any sink node.
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*
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* User: ebanks, rpoplin, mdepristo
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* Date: Mar 23, 2011
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*/
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// Class for finding the K best paths (as determined by the sum of multiplicities of the edges) in a graph.
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// This is different from most graph traversals because we want to test paths from any source node to any sink node.
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public class KBestPaths<T extends BaseVertex> {
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// static access only
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public KBestPaths() { }
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private static int MAX_PATHS_TO_HOLD = 100;
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protected static class MyInt { public int val = 0; }
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// class to keep track of paths
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protected static class Path<T extends BaseVertex> {
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// the last vertex seen in the path
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private final T lastVertex;
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// the list of edges comprising the path
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private final List<BaseEdge> edges;
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// the scores for the path
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private final int totalScore;
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// the graph from which this path originated
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private final BaseGraph<T> graph;
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// used in the bubble state machine to apply Smith-Waterman to the bubble sequence
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// these values were chosen via optimization against the NA12878 knowledge base
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private static final double SW_MATCH = 20.0;
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private static final double SW_MISMATCH = -15.0;
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private static final double SW_GAP = -26.0;
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private static final double SW_GAP_EXTEND = -1.1;
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private static final byte[] STARTING_SW_ANCHOR_BYTES = "XXXXXXXXX".getBytes();
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public Path( final T initialVertex, final BaseGraph<T> graph ) {
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lastVertex = initialVertex;
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edges = new ArrayList<BaseEdge>(0);
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totalScore = 0;
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this.graph = graph;
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}
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public Path( final Path<T> p, final BaseEdge edge ) {
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if( !p.graph.getEdgeSource(edge).equals(p.lastVertex) ) { throw new IllegalStateException("Edges added to path must be contiguous."); }
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graph = p.graph;
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lastVertex = p.graph.getEdgeTarget(edge);
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edges = new ArrayList<BaseEdge>(p.edges);
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edges.add(edge);
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totalScore = p.totalScore + edge.getMultiplicity();
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}
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/**
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* Does this path contain the given edge
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* @param edge the given edge to test
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* @return true if the edge is found in this path
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*/
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public boolean containsEdge( final BaseEdge edge ) {
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if( edge == null ) { throw new IllegalArgumentException("Attempting to test null edge."); }
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for( final BaseEdge e : edges ) {
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if( e.equals(graph, edge) ) {
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return true;
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}
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}
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return false;
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}
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/**
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* Calculate the number of times this edge appears in the path
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* @param edge the given edge to test
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* @return number of times this edge appears in the path
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*/
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public int numInPath( final BaseEdge edge ) {
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if( edge == null ) { throw new IllegalArgumentException("Attempting to test null edge."); }
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int numInPath = 0;
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for( final BaseEdge e : edges ) {
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if( e.equals(graph, edge) ) {
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numInPath++;
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}
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}
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return numInPath;
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}
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public List<BaseEdge> getEdges() { return edges; }
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public int getScore() { return totalScore; }
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public T getLastVertexInPath() { return lastVertex; }
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/**
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* The base sequence for this path. Pull the full sequence for source nodes and then the suffix for all subsequent nodes
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* @return non-null sequence of bases corresponding to this path
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*/
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@Ensures({"result != null"})
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public byte[] getBases() {
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if( edges.size() == 0 ) { return graph.getAdditionalSequence(lastVertex); }
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byte[] bases = graph.getAdditionalSequence(graph.getEdgeSource(edges.get(0)));
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for( final BaseEdge e : edges ) {
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bases = ArrayUtils.addAll(bases, graph.getAdditionalSequence(graph.getEdgeTarget(e)));
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}
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return bases;
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}
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/**
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* Calculate the cigar string for this path using a bubble traversal of the assembly graph and running a Smith-Waterman alignment on each bubble
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* @return non-null Cigar string with reference length equal to the refHaplotype's reference length
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*/
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@Ensures("result != null")
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public Cigar calculateCigar() {
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final Cigar cigar = new Cigar();
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// special case for paths that start on reference but not at the reference source node
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if( edges.get(0).isRef() && !graph.isRefSource(edges.get(0)) ) {
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for( final CigarElement ce : calculateCigarForCompleteBubble(null, null, graph.getEdgeSource(edges.get(0))).getCigarElements() ) {
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cigar.add(ce);
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}
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}
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// reset the bubble state machine
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final BubbleStateMachine<T> bsm = new BubbleStateMachine<T>(cigar);
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for( final BaseEdge e : edges ) {
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if( e.equals(graph, edges.get(0)) ) {
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advanceBubbleStateMachine( bsm, graph.getEdgeSource(e), null );
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}
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advanceBubbleStateMachine( bsm, graph.getEdgeTarget(e), e );
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}
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// special case for paths that don't end on reference
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if( bsm.inBubble ) {
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for( final CigarElement ce : calculateCigarForCompleteBubble(bsm.bubbleBytes, bsm.lastSeenReferenceNode, null).getCigarElements() ) {
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bsm.cigar.add(ce);
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}
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} else if( edges.get(edges.size()-1).isRef() && !graph.isRefSink(edges.get(edges.size()-1)) ) { // special case for paths that end of the reference but haven't completed the entire reference circuit
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for( final CigarElement ce : calculateCigarForCompleteBubble(bsm.bubbleBytes, graph.getEdgeTarget(edges.get(edges.size()-1)), null).getCigarElements() ) {
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bsm.cigar.add(ce);
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}
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}
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return AlignmentUtils.consolidateCigar(bsm.cigar);
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}
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/**
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* Advance the bubble state machine by incorporating the next node in the path.
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* @param bsm the current bubble state machine
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* @param node the node to be incorporated
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* @param e the edge which generated this node in the path
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*/
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@Requires({"bsm != null", "graph != null", "node != null"})
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private void advanceBubbleStateMachine( final BubbleStateMachine<T> bsm, final T node, final BaseEdge e ) {
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if( graph.isReferenceNode( node ) ) {
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if( !bsm.inBubble ) { // just add the ref bases as M's in the Cigar string, and don't do anything else
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if( e !=null && !e.isRef() ) {
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if( graph.referencePathExists( graph.getEdgeSource(e), node) ) {
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for( final CigarElement ce : calculateCigarForCompleteBubble(null, graph.getEdgeSource(e), node).getCigarElements() ) {
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bsm.cigar.add(ce);
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}
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bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.M) );
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} else if ( graph.getEdgeSource(e).equals(graph.getEdgeTarget(e)) ) { // alt edge at ref node points to itself
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bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.I) );
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} else {
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bsm.inBubble = true;
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bsm.bubbleBytes = null;
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bsm.lastSeenReferenceNode = graph.getEdgeSource(e);
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bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
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}
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} else {
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bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.M) );
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}
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} else if( bsm.lastSeenReferenceNode != null && !graph.referencePathExists( bsm.lastSeenReferenceNode, node ) ) { // add bases to the bubble string until we get back to the reference path
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bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
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} else { // close the bubble and use a local SW to determine the Cigar string
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for( final CigarElement ce : calculateCigarForCompleteBubble(bsm.bubbleBytes, bsm.lastSeenReferenceNode, node).getCigarElements() ) {
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bsm.cigar.add(ce);
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}
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bsm.inBubble = false;
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bsm.bubbleBytes = null;
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bsm.lastSeenReferenceNode = null;
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bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.M) );
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}
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} else { // non-ref vertex
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if( bsm.inBubble ) { // just keep accumulating until we get back to the reference path
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bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
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} else { // open up a bubble
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bsm.inBubble = true;
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bsm.bubbleBytes = null;
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bsm.lastSeenReferenceNode = (e != null ? graph.getEdgeSource(e) : null );
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bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
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}
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}
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}
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/**
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* Now that we have a completed bubble run a Smith-Waterman alignment to determine the cigar string for this bubble
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* @param bubbleBytes the bytes that comprise the alternate allele path in this bubble
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* @param fromVertex the vertex that marks the beginning of the reference path in this bubble (null indicates ref source vertex)
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* @param toVertex the vertex that marks the end of the reference path in this bubble (null indicates ref sink vertex)
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* @return the cigar string generated by running a SW alignment between the reference and alternate paths in this bubble
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*/
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@Requires({"graph != null"})
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@Ensures({"result != null"})
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private Cigar calculateCigarForCompleteBubble( final byte[] bubbleBytes, final T fromVertex, final T toVertex ) {
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final byte[] refBytes = graph.getReferenceBytes(fromVertex == null ? graph.getReferenceSourceVertex() : fromVertex, toVertex == null ? graph.getReferenceSinkVertex() : toVertex, fromVertex == null, toVertex == null);
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final Cigar returnCigar = new Cigar();
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// add padding to anchor ref/alt bases in the SW matrix
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byte[] padding = STARTING_SW_ANCHOR_BYTES;
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boolean goodAlignment = false;
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SWPairwiseAlignment swConsensus = null;
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while( !goodAlignment && padding.length < 1000 ) {
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padding = ArrayUtils.addAll(padding, padding); // double the size of the padding each time
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final byte[] reference = ArrayUtils.addAll( ArrayUtils.addAll(padding, refBytes), padding );
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final byte[] alternate = ArrayUtils.addAll( ArrayUtils.addAll(padding, bubbleBytes), padding );
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swConsensus = new SWPairwiseAlignment( reference, alternate, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );
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if( swConsensus.getAlignmentStart2wrt1() == 0 && !swConsensus.getCigar().toString().contains("S") && swConsensus.getCigar().getReferenceLength() == reference.length ) {
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goodAlignment = true;
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}
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}
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if( !goodAlignment ) {
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returnCigar.add(new CigarElement(1, CigarOperator.N));
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return returnCigar;
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}
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final Cigar swCigar = swConsensus.getCigar();
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if( swCigar.numCigarElements() > 6 ) { // this bubble is too divergent from the reference
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returnCigar.add(new CigarElement(1, CigarOperator.N));
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} else {
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for( int iii = 0; iii < swCigar.numCigarElements(); iii++ ) {
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// now we need to remove the padding from the cigar string
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int length = swCigar.getCigarElement(iii).getLength();
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if( iii == 0 ) { length -= padding.length; }
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if( iii == swCigar.numCigarElements() - 1 ) { length -= padding.length; }
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if( length > 0 ) {
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returnCigar.add(new CigarElement(length, swCigar.getCigarElement(iii).getOperator()));
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}
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}
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if( (refBytes == null && returnCigar.getReferenceLength() != 0) || ( refBytes != null && returnCigar.getReferenceLength() != refBytes.length ) ) {
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throw new IllegalStateException("SmithWaterman cigar failure: " + (refBytes == null ? "-" : new String(refBytes)) + " against " + new String(bubbleBytes) + " = " + swConsensus.getCigar());
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}
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}
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return returnCigar;
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}
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// class to keep track of the bubble state machine
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protected static class BubbleStateMachine<T extends BaseVertex> {
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public boolean inBubble = false;
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public byte[] bubbleBytes = null;
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public T lastSeenReferenceNode = null;
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public Cigar cigar = null;
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public BubbleStateMachine( final Cigar initialCigar ) {
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inBubble = false;
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bubbleBytes = null;
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lastSeenReferenceNode = null;
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cigar = initialCigar;
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}
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}
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}
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/**
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* Compare paths such that paths with greater weight are earlier in a list
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*/
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protected static class PathComparatorTotalScore implements Comparator<Path>, Serializable {
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@Override
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public int compare(final Path path1, final Path path2) {
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return path1.totalScore - path2.totalScore;
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return path2.getScore() - path1.getScore();
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}
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}
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/**
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* @see #getKBestPaths(BaseGraph, int) retriving the first 1000 paths
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*/
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public List<Path<T>> getKBestPaths( final BaseGraph<T> graph ) {
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return getKBestPaths(graph, 1000);
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}
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/**
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* Traverse the graph and pull out the best k paths.
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* Paths are scored via their comparator function. The default being PathComparatorTotalScore()
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@ -341,51 +92,41 @@ public class KBestPaths<T extends BaseVertex> {
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* @return a list with at most k top-scoring paths from the graph
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*/
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@Ensures({"result != null", "result.size() <= k"})
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public List<Path> getKBestPaths( final BaseGraph<T> graph, final int k ) {
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public List<Path<T>> getKBestPaths( final BaseGraph<T> graph, final int k ) {
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if( graph == null ) { throw new IllegalArgumentException("Attempting to traverse a null graph."); }
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if( k > MAX_PATHS_TO_HOLD/2 ) { throw new IllegalArgumentException("Asked for more paths than internal parameters allow for."); }
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final ArrayList<Path> bestPaths = new ArrayList<Path>();
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// a min max queue that will collect the best k paths
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final MinMaxPriorityQueue<Path<T>> bestPaths = MinMaxPriorityQueue.orderedBy(new PathComparatorTotalScore()).maximumSize(k).create();
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// run a DFS for best paths
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for( final T v : graph.vertexSet() ) {
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if( graph.inDegreeOf(v) == 0 ) {
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findBestPaths(new Path(v, graph), bestPaths);
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for ( final T v : graph.vertexSet() ) {
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if ( graph.inDegreeOf(v) == 0 ) {
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findBestPaths(new Path<T>(v, graph), bestPaths, new MyInt());
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}
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}
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Collections.sort(bestPaths, new PathComparatorTotalScore() );
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Collections.reverse(bestPaths);
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return bestPaths.subList(0, Math.min(k, bestPaths.size()));
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// the MinMaxPriorityQueue iterator returns items in an arbitrary order, so we need to sort the final result
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final List<Path<T>> toReturn = new ArrayList<Path<T>>(bestPaths);
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Collections.sort(toReturn, new PathComparatorTotalScore());
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return toReturn;
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}
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private void findBestPaths( final Path path, final List<Path> bestPaths ) {
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findBestPaths(path, bestPaths, new MyInt());
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}
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private void findBestPaths( final Path path, final List<Path> bestPaths, final MyInt n ) {
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private void findBestPaths( final Path<T> path, final MinMaxPriorityQueue<Path<T>> bestPaths, final MyInt n ) {
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// did we hit the end of a path?
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if ( allOutgoingEdgesHaveBeenVisited(path) ) {
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if ( bestPaths.size() >= MAX_PATHS_TO_HOLD ) {
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// clean out some low scoring paths
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Collections.sort(bestPaths, new PathComparatorTotalScore() );
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for(int iii = 0; iii < 20; iii++) { bestPaths.remove(0); } // BUGBUG: assumes MAX_PATHS_TO_HOLD >> 20
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}
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bestPaths.add(path);
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} else if( n.val > 10000) {
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// do nothing, just return
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} else if( n.val > 10000 ) {
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// do nothing, just return, as we've done too much work already
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} else {
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// recursively run DFS
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final ArrayList<BaseEdge> edgeArrayList = new ArrayList<BaseEdge>();
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edgeArrayList.addAll(path.graph.outgoingEdgesOf(path.lastVertex));
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final ArrayList<BaseEdge> edgeArrayList = new ArrayList<BaseEdge>(path.getOutgoingEdgesOfLastVertex());
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Collections.sort(edgeArrayList, new BaseEdge.EdgeWeightComparator());
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for ( final BaseEdge edge : edgeArrayList ) {
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// make sure the edge is not already in the path
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if ( path.containsEdge(edge) )
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continue;
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final Path newPath = new Path(path, edge);
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final Path<T> newPath = new Path<T>(path, edge);
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n.val++;
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findBestPaths(newPath, bestPaths, n);
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}
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@ -393,11 +134,15 @@ public class KBestPaths<T extends BaseVertex> {
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}
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/**
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* Have all of the outgoing edges of the final vertex been visited?
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*
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* I.e., are all outgoing vertices of the current path in the list of edges of the graph?
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*
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* @param path the path to test
|
||||
* @return true if all the outgoing edges at the end of this path have already been visited
|
||||
*/
|
||||
private boolean allOutgoingEdgesHaveBeenVisited( final Path<T> path ) {
|
||||
for( final BaseEdge edge : path.graph.outgoingEdgesOf(path.lastVertex) ) {
|
||||
for( final BaseEdge edge : path.getOutgoingEdgesOfLastVertex() ) {
|
||||
if( !path.containsEdge(edge) ) { // TODO -- investigate allowing numInPath < 2 to allow cycles
|
||||
return false;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,394 @@
|
|||
/*
|
||||
* By downloading the PROGRAM you agree to the following terms of use:
|
||||
*
|
||||
* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
|
||||
*
|
||||
* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
|
||||
*
|
||||
* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
|
||||
* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
|
||||
* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
|
||||
*
|
||||
* 1. DEFINITIONS
|
||||
* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
|
||||
*
|
||||
* 2. LICENSE
|
||||
* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
|
||||
* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
|
||||
* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
|
||||
* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
|
||||
*
|
||||
* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
|
||||
* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
|
||||
* Copyright 2012 Broad Institute, Inc.
|
||||
* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
|
||||
* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
|
||||
*
|
||||
* 4. INDEMNIFICATION
|
||||
* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
|
||||
*
|
||||
* 5. NO REPRESENTATIONS OR WARRANTIES
|
||||
* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
|
||||
* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
|
||||
*
|
||||
* 6. ASSIGNMENT
|
||||
* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
|
||||
*
|
||||
* 7. MISCELLANEOUS
|
||||
* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
|
||||
* 7.2 Termination. LICENSEE shall have the right to terminate this Agreement for any reason upon prior written notice to BROAD. If LICENSEE breaches any provision hereunder, and fails to cure such breach within thirty (30) days, BROAD may terminate this Agreement immediately. Upon termination, LICENSEE shall provide BROAD with written assurance that the original and all copies of the PROGRAM have been destroyed, except that, upon prior written authorization from BROAD, LICENSEE may retain a copy for archive purposes.
|
||||
* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
|
||||
* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
|
||||
* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
|
||||
* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
|
||||
* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
|
||||
|
||||
import com.google.java.contract.Ensures;
|
||||
import com.google.java.contract.Requires;
|
||||
import net.sf.samtools.Cigar;
|
||||
import net.sf.samtools.CigarElement;
|
||||
import net.sf.samtools.CigarOperator;
|
||||
import org.apache.commons.lang.ArrayUtils;
|
||||
import org.broadinstitute.sting.utils.SWPairwiseAlignment;
|
||||
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* A path thought a BaseGraph
|
||||
*
|
||||
* class to keep track of paths
|
||||
*
|
||||
* User: depristo
|
||||
* Date: 3/19/13
|
||||
* Time: 2:34 PM
|
||||
*
|
||||
*/
|
||||
class Path<T extends BaseVertex> {
|
||||
// the last vertex seen in the path
|
||||
private final T lastVertex;
|
||||
|
||||
// the list of edges comprising the path
|
||||
private Set<BaseEdge> edgesAsSet = null;
|
||||
private final LinkedList<BaseEdge> edgesInOrder;
|
||||
|
||||
// the scores for the path
|
||||
private final int totalScore;
|
||||
|
||||
// the graph from which this path originated
|
||||
private final BaseGraph<T> graph;
|
||||
|
||||
// used in the bubble state machine to apply Smith-Waterman to the bubble sequence
|
||||
// these values were chosen via optimization against the NA12878 knowledge base
|
||||
private static final double SW_MATCH = 20.0;
|
||||
private static final double SW_MISMATCH = -15.0;
|
||||
private static final double SW_GAP = -26.0;
|
||||
private static final double SW_GAP_EXTEND = -1.1;
|
||||
private static final byte[] STARTING_SW_ANCHOR_BYTES = "XXXXXXXXX".getBytes();
|
||||
|
||||
/**
|
||||
* Create a new Path containing no edges and starting at initialVertex
|
||||
* @param initialVertex the starting vertex of the path
|
||||
* @param graph the graph this path with follow through
|
||||
*/
|
||||
public Path(final T initialVertex, final BaseGraph<T> graph) {
|
||||
if ( initialVertex == null ) throw new IllegalArgumentException("initialVertex cannot be null");
|
||||
if ( graph == null ) throw new IllegalArgumentException("graph cannot be null");
|
||||
if ( ! graph.containsVertex(initialVertex) ) throw new IllegalArgumentException("Vertex " + initialVertex + " must be part of graph " + graph);
|
||||
|
||||
lastVertex = initialVertex;
|
||||
edgesInOrder = new LinkedList<BaseEdge>();
|
||||
totalScore = 0;
|
||||
this.graph = graph;
|
||||
}
|
||||
|
||||
/**
|
||||
* Create a new Path extending p with edge
|
||||
*
|
||||
* @param p the path to extend
|
||||
* @param edge the edge to extend path by
|
||||
*/
|
||||
public Path(final Path<T> p, final BaseEdge edge) {
|
||||
if ( p == null ) throw new IllegalArgumentException("Path cannot be null");
|
||||
if ( edge == null ) throw new IllegalArgumentException("Edge cannot be null");
|
||||
if ( ! p.graph.containsEdge(edge) ) throw new IllegalArgumentException("Graph must contain edge " + edge + " but it doesn't");
|
||||
if ( ! p.graph.getEdgeSource(edge).equals(p.lastVertex) ) { throw new IllegalStateException("Edges added to path must be contiguous."); }
|
||||
|
||||
graph = p.graph;
|
||||
lastVertex = p.graph.getEdgeTarget(edge);
|
||||
edgesInOrder = new LinkedList<BaseEdge>(p.getEdges());
|
||||
edgesInOrder.add(edge);
|
||||
totalScore = p.totalScore + edge.getMultiplicity();
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the collection of edges leaving the last vertex of this path
|
||||
* @return a non-null collection
|
||||
*/
|
||||
public Collection<BaseEdge> getOutgoingEdgesOfLastVertex() {
|
||||
return getGraph().outgoingEdgesOf(getLastVertex());
|
||||
}
|
||||
|
||||
/**
|
||||
* Does this path contain the given edge
|
||||
* @param edge the given edge to test
|
||||
* @return true if the edge is found in this path
|
||||
*/
|
||||
public boolean containsEdge( final BaseEdge edge ) {
|
||||
if( edge == null ) { throw new IllegalArgumentException("Attempting to test null edge."); }
|
||||
if ( edgesInOrder.isEmpty() ) return false;
|
||||
|
||||
// initialize contains cache if necessary
|
||||
if ( edgesAsSet == null ) edgesAsSet = new HashSet<BaseEdge>(edgesInOrder);
|
||||
return edgesAsSet.contains(edge);
|
||||
}
|
||||
|
||||
/**
|
||||
* Check that two paths have the same edges and total score
|
||||
* @param path the other path we might be the same as
|
||||
* @return true if this and path are the same
|
||||
*/
|
||||
protected boolean pathsAreTheSame(Path<T> path) {
|
||||
return totalScore == path.totalScore && edgesInOrder.equals(path.edgesInOrder);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
final StringBuilder b = new StringBuilder("Path{score=" + totalScore + ", path=");
|
||||
boolean first = true;
|
||||
for ( final T v : getVertices() ) {
|
||||
if ( first ) {
|
||||
b.append(" -> ");
|
||||
first = false;
|
||||
}
|
||||
b.append(v.getSequenceString());
|
||||
}
|
||||
return b.toString();
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the graph of this path
|
||||
* @return a non-null graph
|
||||
*/
|
||||
@Ensures("result != null")
|
||||
public BaseGraph<T> getGraph() {
|
||||
return graph;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the edges of this path in order
|
||||
* @return a non-null list of edges
|
||||
*/
|
||||
@Ensures("result != null")
|
||||
public List<BaseEdge> getEdges() { return edgesInOrder; }
|
||||
|
||||
/**
|
||||
* Get the list of vertices in this path in order defined by the edges of the path
|
||||
* @return a non-null, non-empty list of vertices
|
||||
*/
|
||||
@Ensures({"result != null", "!result.isEmpty()"})
|
||||
public List<T> getVertices() {
|
||||
if ( getEdges().isEmpty() )
|
||||
return Collections.singletonList(lastVertex);
|
||||
else {
|
||||
final LinkedList<T> vertices = new LinkedList<T>();
|
||||
boolean first = true;
|
||||
for ( final BaseEdge e : getEdges() ) {
|
||||
if ( first ) {
|
||||
vertices.add(graph.getEdgeSource(e));
|
||||
first = false;
|
||||
}
|
||||
vertices.add(graph.getEdgeTarget(e));
|
||||
}
|
||||
return vertices;
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the total score of this path (bigger is better)
|
||||
* @return a positive integer
|
||||
*/
|
||||
@Ensures("result >= 0")
|
||||
public int getScore() { return totalScore; }
|
||||
|
||||
/**
|
||||
* Get the final vertex of the path
|
||||
* @return a non-null vertex
|
||||
*/
|
||||
@Ensures("result != null")
|
||||
public T getLastVertex() { return lastVertex; }
|
||||
|
||||
/**
|
||||
* The base sequence for this path. Pull the full sequence for source nodes and then the suffix for all subsequent nodes
|
||||
* @return non-null sequence of bases corresponding to this path
|
||||
*/
|
||||
@Ensures({"result != null"})
|
||||
public byte[] getBases() {
|
||||
if( getEdges().isEmpty() ) { return graph.getAdditionalSequence(lastVertex); }
|
||||
|
||||
byte[] bases = graph.getAdditionalSequence(graph.getEdgeSource(edgesInOrder.getFirst()));
|
||||
for( final BaseEdge e : edgesInOrder ) {
|
||||
bases = ArrayUtils.addAll(bases, graph.getAdditionalSequence(graph.getEdgeTarget(e)));
|
||||
}
|
||||
return bases;
|
||||
}
|
||||
|
||||
/**
|
||||
* Calculate the cigar string for this path using a bubble traversal of the assembly graph and running a Smith-Waterman alignment on each bubble
|
||||
* @return non-null Cigar string with reference length equal to the refHaplotype's reference length
|
||||
*/
|
||||
@Ensures("result != null")
|
||||
public Cigar calculateCigar() {
|
||||
final Cigar cigar = new Cigar();
|
||||
// special case for paths that start on reference but not at the reference source node
|
||||
if( edgesInOrder.getFirst().isRef() && !graph.isRefSource(edgesInOrder.getFirst()) ) {
|
||||
for( final CigarElement ce : calculateCigarForCompleteBubble(null, null, graph.getEdgeSource(edgesInOrder.getFirst())).getCigarElements() ) {
|
||||
cigar.add(ce);
|
||||
}
|
||||
}
|
||||
|
||||
// reset the bubble state machine
|
||||
final BubbleStateMachine<T> bsm = new BubbleStateMachine<T>(cigar);
|
||||
|
||||
for( final BaseEdge e : getEdges() ) {
|
||||
if( e.equals(graph, edgesInOrder.getFirst()) ) {
|
||||
advanceBubbleStateMachine( bsm, graph.getEdgeSource(e), null );
|
||||
}
|
||||
advanceBubbleStateMachine( bsm, graph.getEdgeTarget(e), e );
|
||||
}
|
||||
|
||||
// special case for paths that don't end on reference
|
||||
if( bsm.inBubble ) {
|
||||
for( final CigarElement ce : calculateCigarForCompleteBubble(bsm.bubbleBytes, bsm.lastSeenReferenceNode, null).getCigarElements() ) {
|
||||
bsm.cigar.add(ce);
|
||||
}
|
||||
} else if( edgesInOrder.getLast().isRef() && !graph.isRefSink(edgesInOrder.getLast()) ) { // special case for paths that end of the reference but haven't completed the entire reference circuit
|
||||
for( final CigarElement ce : calculateCigarForCompleteBubble(bsm.bubbleBytes, graph.getEdgeTarget(edgesInOrder.getLast()), null).getCigarElements() ) {
|
||||
bsm.cigar.add(ce);
|
||||
}
|
||||
}
|
||||
|
||||
return AlignmentUtils.consolidateCigar(bsm.cigar);
|
||||
}
|
||||
|
||||
/**
|
||||
* Advance the bubble state machine by incorporating the next node in the path.
|
||||
* @param bsm the current bubble state machine
|
||||
* @param node the node to be incorporated
|
||||
* @param e the edge which generated this node in the path
|
||||
*/
|
||||
@Requires({"bsm != null", "graph != null", "node != null"})
|
||||
private void advanceBubbleStateMachine( final BubbleStateMachine<T> bsm, final T node, final BaseEdge e ) {
|
||||
if( graph.isReferenceNode( node ) ) {
|
||||
if( !bsm.inBubble ) { // just add the ref bases as M's in the Cigar string, and don't do anything else
|
||||
if( e !=null && !e.isRef() ) {
|
||||
if( graph.referencePathExists( graph.getEdgeSource(e), node) ) {
|
||||
for( final CigarElement ce : calculateCigarForCompleteBubble(null, graph.getEdgeSource(e), node).getCigarElements() ) {
|
||||
bsm.cigar.add(ce);
|
||||
}
|
||||
bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.M) );
|
||||
} else if ( graph.getEdgeSource(e).equals(graph.getEdgeTarget(e)) ) { // alt edge at ref node points to itself
|
||||
bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.I) );
|
||||
} else {
|
||||
bsm.inBubble = true;
|
||||
bsm.bubbleBytes = null;
|
||||
bsm.lastSeenReferenceNode = graph.getEdgeSource(e);
|
||||
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
|
||||
}
|
||||
} else {
|
||||
bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.M) );
|
||||
}
|
||||
} else if( bsm.lastSeenReferenceNode != null && !graph.referencePathExists( bsm.lastSeenReferenceNode, node ) ) { // add bases to the bubble string until we get back to the reference path
|
||||
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
|
||||
} else { // close the bubble and use a local SW to determine the Cigar string
|
||||
for( final CigarElement ce : calculateCigarForCompleteBubble(bsm.bubbleBytes, bsm.lastSeenReferenceNode, node).getCigarElements() ) {
|
||||
bsm.cigar.add(ce);
|
||||
}
|
||||
bsm.inBubble = false;
|
||||
bsm.bubbleBytes = null;
|
||||
bsm.lastSeenReferenceNode = null;
|
||||
bsm.cigar.add( new CigarElement( graph.getAdditionalSequence(node).length, CigarOperator.M) );
|
||||
}
|
||||
} else { // non-ref vertex
|
||||
if( bsm.inBubble ) { // just keep accumulating until we get back to the reference path
|
||||
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
|
||||
} else { // open up a bubble
|
||||
bsm.inBubble = true;
|
||||
bsm.bubbleBytes = null;
|
||||
bsm.lastSeenReferenceNode = (e != null ? graph.getEdgeSource(e) : null );
|
||||
bsm.bubbleBytes = ArrayUtils.addAll( bsm.bubbleBytes, graph.getAdditionalSequence(node) );
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Now that we have a completed bubble run a Smith-Waterman alignment to determine the cigar string for this bubble
|
||||
* @param bubbleBytes the bytes that comprise the alternate allele path in this bubble
|
||||
* @param fromVertex the vertex that marks the beginning of the reference path in this bubble (null indicates ref source vertex)
|
||||
* @param toVertex the vertex that marks the end of the reference path in this bubble (null indicates ref sink vertex)
|
||||
* @return the cigar string generated by running a SW alignment between the reference and alternate paths in this bubble
|
||||
*/
|
||||
@Requires({"graph != null"})
|
||||
@Ensures({"result != null"})
|
||||
private Cigar calculateCigarForCompleteBubble( final byte[] bubbleBytes, final T fromVertex, final T toVertex ) {
|
||||
final byte[] refBytes = graph.getReferenceBytes(fromVertex == null ? graph.getReferenceSourceVertex() : fromVertex, toVertex == null ? graph.getReferenceSinkVertex() : toVertex, fromVertex == null, toVertex == null);
|
||||
|
||||
final Cigar returnCigar = new Cigar();
|
||||
|
||||
// add padding to anchor ref/alt bases in the SW matrix
|
||||
byte[] padding = STARTING_SW_ANCHOR_BYTES;
|
||||
boolean goodAlignment = false;
|
||||
SWPairwiseAlignment swConsensus = null;
|
||||
while( !goodAlignment && padding.length < 1000 ) {
|
||||
padding = ArrayUtils.addAll(padding, padding); // double the size of the padding each time
|
||||
final byte[] reference = ArrayUtils.addAll( ArrayUtils.addAll(padding, refBytes), padding );
|
||||
final byte[] alternate = ArrayUtils.addAll( ArrayUtils.addAll(padding, bubbleBytes), padding );
|
||||
swConsensus = new SWPairwiseAlignment( reference, alternate, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );
|
||||
if( swConsensus.getAlignmentStart2wrt1() == 0 && !swConsensus.getCigar().toString().contains("S") && swConsensus.getCigar().getReferenceLength() == reference.length ) {
|
||||
goodAlignment = true;
|
||||
}
|
||||
}
|
||||
if( !goodAlignment ) {
|
||||
returnCigar.add(new CigarElement(1, CigarOperator.N));
|
||||
return returnCigar;
|
||||
}
|
||||
|
||||
final Cigar swCigar = swConsensus.getCigar();
|
||||
if( swCigar.numCigarElements() > 6 ) { // this bubble is too divergent from the reference
|
||||
returnCigar.add(new CigarElement(1, CigarOperator.N));
|
||||
} else {
|
||||
for( int iii = 0; iii < swCigar.numCigarElements(); iii++ ) {
|
||||
// now we need to remove the padding from the cigar string
|
||||
int length = swCigar.getCigarElement(iii).getLength();
|
||||
if( iii == 0 ) { length -= padding.length; }
|
||||
if( iii == swCigar.numCigarElements() - 1 ) { length -= padding.length; }
|
||||
if( length > 0 ) {
|
||||
returnCigar.add(new CigarElement(length, swCigar.getCigarElement(iii).getOperator()));
|
||||
}
|
||||
}
|
||||
if( (refBytes == null && returnCigar.getReferenceLength() != 0) || ( refBytes != null && returnCigar.getReferenceLength() != refBytes.length ) ) {
|
||||
throw new IllegalStateException("SmithWaterman cigar failure: " + (refBytes == null ? "-" : new String(refBytes)) + " against " + new String(bubbleBytes) + " = " + swConsensus.getCigar());
|
||||
}
|
||||
}
|
||||
|
||||
return returnCigar;
|
||||
}
|
||||
|
||||
// class to keep track of the bubble state machine
|
||||
private static class BubbleStateMachine<T extends BaseVertex> {
|
||||
public boolean inBubble = false;
|
||||
public byte[] bubbleBytes = null;
|
||||
public T lastSeenReferenceNode = null;
|
||||
public Cigar cigar = null;
|
||||
|
||||
public BubbleStateMachine( final Cigar initialCigar ) {
|
||||
inBubble = false;
|
||||
bubbleBytes = null;
|
||||
lastSeenReferenceNode = null;
|
||||
cigar = initialCigar;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -55,9 +55,9 @@ import org.testng.Assert;
|
|||
import org.testng.annotations.DataProvider;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.LinkedList;
|
||||
import java.util.List;
|
||||
|
||||
/**
|
||||
|
|
@ -67,6 +67,72 @@ import java.util.List;
|
|||
*/
|
||||
|
||||
public class KBestPathsUnitTest {
|
||||
@DataProvider(name = "BasicPathFindingData")
|
||||
public Object[][] makeBasicPathFindingData() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
// for ( final int nStartNodes : Arrays.asList(1) ) {
|
||||
// for ( final int nBranchesPerBubble : Arrays.asList(2) ) {
|
||||
// for ( final int nEndNodes : Arrays.asList(1) ) {
|
||||
// for ( final boolean addCycle : Arrays.asList(true) ) {
|
||||
for ( final int nStartNodes : Arrays.asList(1, 2, 3) ) {
|
||||
for ( final int nBranchesPerBubble : Arrays.asList(2, 3) ) {
|
||||
for ( final int nEndNodes : Arrays.asList(1, 2, 3) ) {
|
||||
for ( final boolean addCycle : Arrays.asList(true, false) ) {
|
||||
tests.add(new Object[]{nStartNodes, nBranchesPerBubble, nEndNodes, addCycle});
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
private static int weight = 1;
|
||||
final List<SeqVertex> createVertices(final SeqGraph graph, final int n, final SeqVertex source, final SeqVertex target) {
|
||||
final List<String> seqs = Arrays.asList("A", "C", "G", "T");
|
||||
final List<SeqVertex> vertices = new LinkedList<SeqVertex>();
|
||||
for ( int i = 0; i < n; i++ ) {
|
||||
final SeqVertex v = new SeqVertex(seqs.get(i));
|
||||
graph.addVertex(v);
|
||||
vertices.add(v);
|
||||
if ( source != null ) graph.addEdge(source, v, new BaseEdge(false, weight++));
|
||||
if ( target != null ) graph.addEdge(v, target, new BaseEdge(false, weight++));
|
||||
}
|
||||
return vertices;
|
||||
}
|
||||
|
||||
@Test(dataProvider = "BasicPathFindingData", enabled = true)
|
||||
public void testBasicPathFinding(final int nStartNodes, final int nBranchesPerBubble, final int nEndNodes, final boolean addCycle) {
|
||||
SeqGraph graph = new SeqGraph();
|
||||
|
||||
final SeqVertex middleTop = new SeqVertex("GTAC");
|
||||
final SeqVertex middleBottom = new SeqVertex("ACTG");
|
||||
graph.addVertices(middleTop, middleBottom);
|
||||
final List<SeqVertex> starts = createVertices(graph, nStartNodes, null, middleTop);
|
||||
final List<SeqVertex> bubbles = createVertices(graph, nBranchesPerBubble, middleTop, middleBottom);
|
||||
final List<SeqVertex> ends = createVertices(graph, nEndNodes, middleBottom, null);
|
||||
|
||||
if ( addCycle ) graph.addEdge(middleBottom, middleBottom);
|
||||
|
||||
// enumerate all possible paths
|
||||
final List<Path<SeqVertex>> paths = new KBestPaths<SeqVertex>().getKBestPaths(graph);
|
||||
|
||||
final int expectedNumOfPaths = nStartNodes * nBranchesPerBubble * (addCycle ? 2 : 1) * nEndNodes;
|
||||
Assert.assertEquals(paths.size(), expectedNumOfPaths, "Didn't find the expected number of paths");
|
||||
|
||||
int lastScore = Integer.MAX_VALUE;
|
||||
for ( final Path path : paths ) {
|
||||
Assert.assertTrue(path.getScore() <= lastScore, "Paths out of order. Path " + path + " has score above previous " + lastScore);
|
||||
lastScore = path.getScore();
|
||||
}
|
||||
|
||||
// get the best path, and make sure it's the same as our optimal path overall
|
||||
final Path best = paths.get(0);
|
||||
final List<Path<SeqVertex>> justOne = new KBestPaths<SeqVertex>().getKBestPaths(graph, 1);
|
||||
Assert.assertEquals(justOne.size(), 1);
|
||||
Assert.assertTrue(justOne.get(0).pathsAreTheSame(best), "Best path from complete enumerate " + best + " not the same as from k = 1 search " + justOne.get(0));
|
||||
}
|
||||
|
||||
@DataProvider(name = "BasicBubbleDataProvider")
|
||||
public Object[][] makeBasicBubbleDataProvider() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
|
@ -99,12 +165,10 @@ public class KBestPathsUnitTest {
|
|||
graph.addEdge(v, v2Alt, new BaseEdge(false, 5));
|
||||
graph.addEdge(v2Alt, v3, new BaseEdge(false, 5));
|
||||
|
||||
graph.printGraph(new File("test.dot"), 10);
|
||||
|
||||
// Construct the test path
|
||||
KBestPaths.Path<SeqVertex> path = new KBestPaths.Path<SeqVertex>(v, graph);
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v, v2Alt));
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v2Alt, v3));
|
||||
Path<SeqVertex> path = new Path<SeqVertex>(v, graph);
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v, v2Alt));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v2Alt, v3));
|
||||
|
||||
// Construct the actual cigar string implied by the test path
|
||||
Cigar expectedCigar = new Cigar();
|
||||
|
|
@ -123,52 +187,40 @@ public class KBestPathsUnitTest {
|
|||
Assert.assertEquals(path.calculateCigar().toString(), AlignmentUtils.consolidateCigar(expectedCigar).toString(), "Cigar string mismatch");
|
||||
}
|
||||
|
||||
// TODO -- test block substitution because it doesn't look like it's correct now
|
||||
// @Test(dataProvider = "BasicBubbleDataProvider")
|
||||
// public void testBasicBubbleData(final int refBubbleLength, final int altBubbleLength) {
|
||||
// // Construct the assembly graph
|
||||
// final int KMER_LENGTH = 3;
|
||||
// SeqGraph graph = new SeqGraph(KMER_LENGTH);
|
||||
// final String preRef = "ATGG";
|
||||
// final String postRef = "GGGGC";
|
||||
//
|
||||
// SeqVertex v = new SeqVertex(preRef);
|
||||
// SeqVertex v2Ref = new SeqVertex(Utils.dupString('A', refBubbleLength));
|
||||
// SeqVertex v2Alt = new SeqVertex(Utils.dupString('T', altBubbleLength));
|
||||
// SeqVertex v3 = new SeqVertex(postRef);
|
||||
//
|
||||
// graph.addVertex(v);
|
||||
// graph.addVertex(v2Ref);
|
||||
// graph.addVertex(v2Alt);
|
||||
// graph.addVertex(v3);
|
||||
// graph.addEdge(v, v2Ref, new BaseEdge(true, 10));
|
||||
// graph.addEdge(v2Ref, v3, new BaseEdge(true, 10));
|
||||
// graph.addEdge(v, v2Alt, new BaseEdge(false, 5));
|
||||
// graph.addEdge(v2Alt, v3, new BaseEdge(false, 5));
|
||||
//
|
||||
// graph.printGraph(new File("test.dot"), 10);
|
||||
//
|
||||
// // Construct the test path
|
||||
// KBestPaths.Path<SeqVertex> path = new KBestPaths.Path<SeqVertex>(v, graph);
|
||||
// path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v, v2Alt));
|
||||
// path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v2Alt, v3));
|
||||
//
|
||||
// // Construct the actual cigar string implied by the test path
|
||||
// Cigar expectedCigar = new Cigar();
|
||||
// expectedCigar.add(new CigarElement(preRef.length(), CigarOperator.M));
|
||||
// if( refBubbleLength > altBubbleLength ) {
|
||||
// expectedCigar.add(new CigarElement(altBubbleLength, CigarOperator.M));
|
||||
// expectedCigar.add(new CigarElement(refBubbleLength - altBubbleLength, CigarOperator.D));
|
||||
// } else if ( refBubbleLength < altBubbleLength ) {
|
||||
// expectedCigar.add(new CigarElement(altBubbleLength - refBubbleLength,CigarOperator.I));
|
||||
// expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M));
|
||||
// } else {
|
||||
// expectedCigar.add(new CigarElement(refBubbleLength, CigarOperator.M));
|
||||
// }
|
||||
// expectedCigar.add(new CigarElement(postRef.length() - (KMER_LENGTH - 1), CigarOperator.M));
|
||||
//
|
||||
// Assert.assertEquals(path.calculateCigar().toString(), AlignmentUtils.consolidateCigar(expectedCigar).toString(), "Cigar string mismatch");
|
||||
// }
|
||||
@DataProvider(name = "GetBasesData")
|
||||
public Object[][] makeGetBasesData() {
|
||||
List<Object[]> tests = new ArrayList<Object[]>();
|
||||
|
||||
final List<String> frags = Arrays.asList("ACT", "GAC", "CAT");
|
||||
|
||||
for ( int n = 1; n <= frags.size(); n++ ) {
|
||||
for ( final List<String> comb : Utils.makePermutations(frags, n, false) ) {
|
||||
tests.add(new Object[]{comb});
|
||||
}
|
||||
}
|
||||
return tests.toArray(new Object[][]{});
|
||||
}
|
||||
|
||||
@Test(dataProvider = "GetBasesData", enabled = true)
|
||||
public void testGetBases(final List<String> frags) {
|
||||
// Construct the assembly graph
|
||||
SeqGraph graph = new SeqGraph(3);
|
||||
|
||||
SeqVertex prev = null;
|
||||
for ( int i = 0; i < frags.size(); i++ ) {
|
||||
SeqVertex v = new SeqVertex(frags.get(i));
|
||||
graph.addVertex(v);
|
||||
if ( prev != null )
|
||||
graph.addEdge(prev, v);
|
||||
prev = v;
|
||||
}
|
||||
|
||||
// enumerate all possible paths
|
||||
final List<Path<SeqVertex>> paths = new KBestPaths<SeqVertex>().getKBestPaths(graph);
|
||||
Assert.assertEquals(paths.size(), 1);
|
||||
final Path<SeqVertex> path = paths.get(0);
|
||||
Assert.assertEquals(new String(path.getBases()), Utils.join("", frags), "Path doesn't have the expected sequence");
|
||||
}
|
||||
|
||||
@DataProvider(name = "TripleBubbleDataProvider")
|
||||
public Object[][] makeTripleBubbleDataProvider() {
|
||||
|
|
@ -236,21 +288,19 @@ public class KBestPathsUnitTest {
|
|||
graph.addEdge(v6Alt, v7, new BaseEdge(false, 55));
|
||||
graph.addEdge(v7, postV, new BaseEdge(false, 1));
|
||||
|
||||
graph.printGraph(new File("test.debruijn.dot"), 10);
|
||||
|
||||
// Construct the test path
|
||||
KBestPaths.Path<SeqVertex> path = new KBestPaths.Path<SeqVertex>( (offRefBeginning ? preV : v), graph);
|
||||
Path<SeqVertex> path = new Path<SeqVertex>( (offRefBeginning ? preV : v), graph);
|
||||
if( offRefBeginning ) {
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(preV, v));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(preV, v));
|
||||
}
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v, v2Alt));
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v2Alt, v3));
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v3, v4Ref));
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v4Ref, v5));
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v5, v6Alt));
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v6Alt, v7));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v, v2Alt));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v2Alt, v3));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v3, v4Ref));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v4Ref, v5));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v5, v6Alt));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v6Alt, v7));
|
||||
if( offRefEnding ) {
|
||||
path = new KBestPaths.Path<SeqVertex>(path, graph.getEdge(v7,postV));
|
||||
path = new Path<SeqVertex>(path, graph.getEdge(v7,postV));
|
||||
}
|
||||
|
||||
// Construct the actual cigar string implied by the test path
|
||||
|
|
|
|||
Loading…
Reference in New Issue