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Bugfix for pruning and removing non-reference edges in graph 

-- Previous algorithms were applying pruneGraph inappropriately on the raw sequence graph (where each vertex is a single base).  This results in overpruning of the graph, as prunegraph really relied on the zipping of linear chains (and the sharing of weight this provides) to avoid over-pruning the graph.  Probably we should think hard about this.  This commit fixes this logic, so we zip the graph between pruning
-- In this process ID's a fundamental problem with how we were trimming away vertices that occur on a path from the reference source to sink.  In fact, we were leaving in any vertex that happened to be accessible from source, any vertices in cycles, and any vertex that wasn't the absolute end of a chain going to a sink.  The new algorithm fixes all of this, using a BaseGraphIterator that's a general approach to walking the base graph.  Other routines that use the same traversal idiom refactored to use this iterator.  Added unit tests for all of these capabilities.
-- Created new BaseGraphIterator, which abstracts common access patterns to graph, and use this where appropriate
This commit is contained in:
Mark DePristo 2013-03-24 17:20:30 -04:00
parent 12475cc027
commit 78c672676b
4 changed files with 279 additions and 70 deletions
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128
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/BaseGraph.java
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@ -336,9 +336,18 @@ public class BaseGraph<T extends BaseVertex> extends DefaultDirectedGraph<T, Bas
* @param remaining all additional vertices to connect
*/
public void addEdges(final T start, final T ... remaining) {
addEdges(new BaseEdge(false, 1), start, remaining);
}
/**
* Convenience function to add multiple edges to the graph
* @param start the first vertex to connect
* @param remaining all additional vertices to connect
*/
public void addEdges(final BaseEdge template, final T start, final T ... remaining) {
T prev = start;
for ( final T next : remaining ) {
addEdge(prev, next);
addEdge(prev, next, new BaseEdge(template));
prev = next;
}
}
@ -386,19 +395,15 @@ public class BaseGraph<T extends BaseVertex> extends DefaultDirectedGraph<T, Bas
}
}
// TODO -- generalize to support both types of graphs. Need some kind of display string function
public void printGraph(final PrintStream graphWriter, final boolean writeHeader, final int pruneFactor) {
if ( writeHeader )
graphWriter.println("digraph assemblyGraphs {");
for( final BaseEdge edge : edgeSet() ) {
// if( edge.getMultiplicity() > PRUNE_FACTOR ) {
graphWriter.println("\t" + getEdgeSource(edge).toString() + " -> " + getEdgeTarget(edge).toString() + " [" + (edge.getMultiplicity() <= pruneFactor ? "style=dotted,color=grey," : "") + "label=\"" + edge.getMultiplicity() + "\"];");
// }
if( edge.isRef() ) {
graphWriter.println("\t" + getEdgeSource(edge).toString() + " -> " + getEdgeTarget(edge).toString() + " [color=red];");
}
//if( !edge.isRef() && edge.getMultiplicity() <= PRUNE_FACTOR ) { System.out.println("Graph pruning warning!"); }
}
for( final T v : vertexSet() ) {
@ -436,6 +441,30 @@ public class BaseGraph<T extends BaseVertex> extends DefaultDirectedGraph<T, Bas
edgesToCheck.remove(e);
}
removeSingletonOrphanVertices();
}
/**
* Prune all edges from this graph that have multiplicity <= pruneFactor and remove all orphaned singleton vertices as well
*
* @param pruneFactor all edges with multiplicity <= this factor that aren't ref edges will be removed
*/
protected void pruneGraph( final int pruneFactor ) {
final List<BaseEdge> edgesToRemove = new ArrayList<BaseEdge>();
for( final BaseEdge e : edgeSet() ) {
if( e.getMultiplicity() <= pruneFactor && !e.isRef() ) { // remove non-reference edges with weight less than or equal to the pruning factor
edgesToRemove.add(e);
}
}
removeAllEdges(edgesToRemove);
removeSingletonOrphanVertices();
}
/**
* Remove all vertices in the graph that have in and out degree of 0
*/
protected void removeSingletonOrphanVertices() {
// Run through the graph and clean up singular orphaned nodes
final List<T> verticesToRemove = new LinkedList<T>();
for( final T v : vertexSet() ) {
@ -446,65 +475,54 @@ public class BaseGraph<T extends BaseVertex> extends DefaultDirectedGraph<T, Bas
removeAllVertices(verticesToRemove);
}
/**
* Remove all vertices on the graph that cannot be accessed by following any edge,
* regardless of its direction, from the reference source vertex
*/
public void removeVerticesNotConnectedToRefRegardlessOfEdgeDirection() {
final HashSet<T> toRemove = new HashSet<T>(vertexSet());
final T refV = getReferenceSourceVertex();
if ( refV != null ) {
for ( final T v : new BaseGraphIterator<T>(this, refV, true, true) ) {
toRemove.remove(v);
}
}
removeAllVertices(toRemove);
}
/**
* Remove all vertices in the graph that aren't on a path from the reference source vertex to the reference sink vertex
*
* More aggressive reference pruning algorithm than removeVerticesNotConnectedToRefRegardlessOfEdgeDirection,
* as it requires vertices to not only be connected by a series of directed edges but also prunes away
* paths that do not also meet eventually with the reference sink vertex
*/
protected void removePathsNotConnectedToRef() {
if ( getReferenceSourceVertex() == null || getReferenceSinkVertex() == null ) {
throw new IllegalStateException("Graph must have ref source and sink vertices");
}
// get the set of vertices we can reach by going forward from the ref source
final Set<T> onPathFromRefSource = new HashSet<T>(vertexSet().size());
for ( final T v : new BaseGraphIterator<T>(this, getReferenceSourceVertex(), false, true) ) {
onPathFromRefSource.add(v);
}
// get the set of vertices we can reach by going backward from the ref sink
final Set<T> onPathFromRefSink = new HashSet<T>(vertexSet().size());
for ( final T v : new BaseGraphIterator<T>(this, getReferenceSinkVertex(), true, false) ) {
onPathFromRefSink.add(v);
}
// we want to remove anything that's not in both the sink and source sets
final Set<T> verticesToRemove = new HashSet<T>(vertexSet());
final DepthFirstIterator<T, BaseEdge> dfi = new DepthFirstIterator<T, BaseEdge>(this, getReferenceSourceVertex());
while ( dfi.hasNext() ) {
final T accessibleFromRefSource = dfi.next();
// we also want to prune all sinks that aren't the reference sink
if ( ! isNonRefSink(accessibleFromRefSource) )
verticesToRemove.remove(accessibleFromRefSource);
}
onPathFromRefSource.retainAll(onPathFromRefSink);
verticesToRemove.removeAll(onPathFromRefSource);
removeAllVertices(verticesToRemove);
}
protected void pruneGraph( final int pruneFactor ) {
final List<BaseEdge> edgesToRemove = new ArrayList<BaseEdge>();
for( final BaseEdge e : edgeSet() ) {
if( e.getMultiplicity() <= pruneFactor && !e.isRef() ) { // remove non-reference edges with weight less than or equal to the pruning factor
edgesToRemove.add(e);
}
}
removeAllEdges(edgesToRemove);
// Run through the graph and clean up singular orphaned nodes
final List<T> verticesToRemove = new ArrayList<T>();
for( final T v : vertexSet() ) {
if( inDegreeOf(v) == 0 && outDegreeOf(v) == 0 ) {
verticesToRemove.add(v);
}
}
removeAllVertices(verticesToRemove);
}
public void removeVerticesNotConnectedToRef() {
final HashSet<T> toRemove = new HashSet<T>(vertexSet());
final HashSet<T> visited = new HashSet<T>();
final LinkedList<T> toVisit = new LinkedList<T>();
final T refV = getReferenceSourceVertex();
if ( refV != null ) {
toVisit.add(refV);
while ( ! toVisit.isEmpty() ) {
final T v = toVisit.pop();
if ( ! visited.contains(v) ) {
toRemove.remove(v);
visited.add(v);
for ( final T prev : incomingVerticesOf(v) ) toVisit.add(prev);
for ( final T next : outgoingVerticesOf(v) ) toVisit.add(next);
}
}
removeAllVertices(toRemove);
}
}
/**
* Semi-lenient comparison of two graphs, truing true if g1 and g2 have similar structure
*

120
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/BaseGraphIterator.java 100644
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@ -0,0 +1,120 @@
/*
* 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).
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* 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.
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* 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.
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package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedList;
/**
* General iterator that can iterate over all vertices in a BaseGraph, following either
* incoming, outgoing edge (as well as both or none) edges. Supports traversal of graphs
* with cycles and other crazy structures. Will only ever visit each vertex once. The
* order in which the vertices are visited is undefined.
*
* User: depristo
* Date: 3/24/13
* Time: 4:41 PM
*/
public class BaseGraphIterator<T extends BaseVertex> implements Iterator<T>, Iterable<T> {
final HashSet<T> visited = new HashSet<T>();
final LinkedList<T> toVisit = new LinkedList<T>();
final BaseGraph<T> graph;
final boolean followIncomingEdges, followOutgoingEdges;
/**
* Create a new BaseGraphIterator starting its traversal at start
*
* Note that if both followIncomingEdges and followOutgoingEdges are false, we simply return the
* start vertex
*
* @param graph the graph to iterator over. Cannot be null
* @param start the vertex to start at. Cannot be null
* @param followIncomingEdges should we follow incoming edges during our
* traversal? (goes backward through the graph)
* @param followOutgoingEdges should we follow outgoing edges during out traversal?
*/
public BaseGraphIterator(final BaseGraph<T> graph, final T start,
final boolean followIncomingEdges, final boolean followOutgoingEdges) {
if ( graph == null ) throw new IllegalArgumentException("graph cannot be null");
if ( start == null ) throw new IllegalArgumentException("start cannot be null");
if ( ! graph.containsVertex(start) ) throw new IllegalArgumentException("start " + start + " must be in graph but it isn't");
this.graph = graph;
this.followIncomingEdges = followIncomingEdges;
this.followOutgoingEdges = followOutgoingEdges;
toVisit.add(start);
}
@Override
public Iterator<T> iterator() {
return this;
}
@Override
public boolean hasNext() {
return ! toVisit.isEmpty();
}
@Override
public T next() {
final T v = toVisit.pop();
if ( ! visited.contains(v) ) {
visited.add(v);
if ( followIncomingEdges ) for ( final T prev : graph.incomingVerticesOf(v) ) toVisit.add(prev);
if ( followOutgoingEdges ) for ( final T next : graph.outgoingVerticesOf(v) ) toVisit.add(next);
}
return v;
}
@Override
public void remove() {
throw new UnsupportedOperationException("Doesn't implement remove");
}
}

15
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssembler.java
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@ -183,11 +183,18 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
private SeqGraph toSeqGraph(final DeBruijnGraph deBruijnGraph) {
final SeqGraph seqGraph = deBruijnGraph.convertToSequenceGraph();
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.1.dot"), pruneFactor);
// the very first thing we need to do is zip up the graph, or pruneGraph will be too aggressive
seqGraph.zipLinearChains();
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.2.zipped.dot"), pruneFactor);
// now go through and prune the graph, removing vertices no longer connected to the reference chain
seqGraph.pruneGraph(pruneFactor);
seqGraph.removeVerticesNotConnectedToRef();
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.2.pruned.dot"), pruneFactor);
seqGraph.removeVerticesNotConnectedToRefRegardlessOfEdgeDirection();
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.3.pruned.dot"), pruneFactor);
seqGraph.simplifyGraph();
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.3.merged.dot"), pruneFactor);
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.4.merged.dot"), pruneFactor);
// The graph has degenerated in some way, so the reference source and/or sink cannot be id'd. Can
// happen in cases where for example the reference somehow manages to acquire a cycle, or
@ -196,7 +203,7 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
return null;
seqGraph.removePathsNotConnectedToRef();
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.4.refcleaned.dot"), pruneFactor);
if ( debugGraphTransformations ) seqGraph.printGraph(new File("sequenceGraph.5.refcleaned.dot"), pruneFactor);
return seqGraph;
}

86
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/BaseGraphUnitTest.java
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@ -49,22 +49,12 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
import scala.actors.threadpool.Arrays;
import java.io.File;
import java.util.Collections;
import java.util.HashSet;
import java.util.Set;
import java.util.*;
/**
* Created with IntelliJ IDEA.
* User: depristo
* Date: 3/15/13
* Time: 3:36 PM
* To change this template use File | Settings | File Templates.
*/
public class BaseGraphUnitTest extends BaseTest {
SeqGraph graph;
SeqVertex v1, v2, v3, v4, v5;
@ -105,6 +95,80 @@ public class BaseGraphUnitTest extends BaseTest {
assertVertexSetEquals(graph.incomingVerticesOf(v5), v4);
}
@Test
public void testRemoveSingletonOrphanVertices() throws Exception {
// all vertices in graph are connected
final List<SeqVertex> kept = new LinkedList<SeqVertex>(graph.vertexSet());
final SeqVertex rm1 = new SeqVertex("CAGT");
final SeqVertex rm2 = new SeqVertex("AGTC");
graph.addVertices(rm1, rm2);
Assert.assertEquals(graph.vertexSet().size(), kept.size() + 2);
final BaseEdge rm12e = new BaseEdge(false, 1);
graph.addEdge(rm1, rm2, rm12e);
final SeqGraph original = (SeqGraph)graph.clone();
graph.removeSingletonOrphanVertices();
Assert.assertTrue(BaseGraph.graphEquals(original, graph), "Graph with disconnected component but edges between components shouldn't be modified");
graph.removeEdge(rm12e); // now we should be able to remove rm1 and rm2
graph.removeSingletonOrphanVertices();
Assert.assertTrue(graph.vertexSet().containsAll(kept));
Assert.assertFalse(graph.containsVertex(rm1));
Assert.assertFalse(graph.containsVertex(rm2));
}
@Test
public void testRemovePathsNotConnectedToRef() throws Exception {
final SeqGraph graph = new SeqGraph();
SeqVertex src = new SeqVertex("A");
SeqVertex end = new SeqVertex("A");
SeqVertex g1 = new SeqVertex("C");
SeqVertex g2 = new SeqVertex("G");
SeqVertex g3 = new SeqVertex("T");
SeqVertex g4 = new SeqVertex("AA");
SeqVertex g5 = new SeqVertex("AA");
SeqVertex g6 = new SeqVertex("AA");
SeqVertex g8 = new SeqVertex("AA");
SeqVertex g7 = new SeqVertex("AA");
SeqVertex b1 = new SeqVertex("CC");
SeqVertex b2 = new SeqVertex("GG");
SeqVertex b3 = new SeqVertex("TT");
SeqVertex b4 = new SeqVertex("AAA");
SeqVertex b5 = new SeqVertex("CCC");
SeqVertex b6 = new SeqVertex("GGG");
SeqVertex b7 = new SeqVertex("AAAA");
SeqVertex b8 = new SeqVertex("GGGG");
SeqVertex b9 = new SeqVertex("CCCC");
graph.addVertices(src, end, g1, g2, g3, g4, g5, g6, g7, g8);
graph.addEdges(new BaseEdge(true, 1), src, g1, g2, g4, end);
graph.addEdges(src, g1, g5, g6, g7, end);
graph.addEdges(src, g1, g5, g8, g7, end);
graph.addEdges(src, g1, g3, end);
// the current state of the graph is the good one
final SeqGraph good = (SeqGraph)graph.clone();
// now add the bads to the graph
graph.addVertices(b1, b2, b3, b4, b5, b6, b7, b8, b9);
graph.addEdges(src, b1); // source -> b1 is dead
graph.addEdges(b6, src); // x -> source is bad
graph.addEdges(g4, b2); // off random vertex is bad
graph.addEdges(g3, b3, b4); // two vertices that don't connect to end are bad
graph.addEdges(end, b5); // vertex off end is bad
graph.addEdges(g3, b7, b8, b7); // cycle is bad
graph.addEdges(g3, b9, b9); // self-cycle is bad
final boolean debug = true;
if ( debug ) good.printGraph(new File("expected.dot"), 0);
if ( debug ) graph.printGraph(new File("bad.dot"), 0);
graph.removePathsNotConnectedToRef();
if ( debug ) graph.printGraph(new File("actual.dot"), 0);
Assert.assertTrue(BaseGraph.graphEquals(graph, good), "Failed to remove exactly the bad nodes");
}
@Test
public void testPrintEmptyGraph() throws Exception {
final File tmp = File.createTempFile("tmp", "dot");