Bug fixes plus some debugging code added. Broke out DeBruijnVertex into its own class so that the interface is now cleaner. Still very much a work in progress.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5498 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
37fbf17da8
commit
401d1cb97f
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@ -0,0 +1,71 @@
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package org.broadinstitute.sting.playground.gatk.walkers.assembly;
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import java.util.*;
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/**
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* Created by IntelliJ IDEA.
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* User: ebanks
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* Date: Mar 23, 2011
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*/
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// simple node class for storing kmer sequences
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public class DeBruijnVertex {
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// used for equals()
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protected byte[] actualSequence;
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// used for printing and traversing graphs
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protected byte[] printableSequence;
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public DeBruijnVertex(byte[] sequence) {
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actualSequence = sequence;
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printableSequence = new byte[sequence.length];
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System.arraycopy(sequence, 0, printableSequence, 0, sequence.length);
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}
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public boolean equals(DeBruijnVertex v) {
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return Arrays.equals(actualSequence, v.actualSequence);
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}
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public String toString() {
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return new String(printableSequence);
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}
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public void addPrefix(byte[] prefix, boolean justPrintableSequence) {
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printableSequence = addPrefix(printableSequence, prefix);
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if ( !justPrintableSequence )
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actualSequence = addPrefix(actualSequence, prefix);
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}
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private static byte[] addPrefix(byte[] sequence, byte[] prefix) {
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byte[] newSequence = new byte[sequence.length + prefix.length];
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System.arraycopy(prefix, 0, newSequence, 0, prefix.length);
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System.arraycopy(sequence, 0, newSequence, prefix.length, sequence.length);
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return newSequence;
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}
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public void removePrefix(int prefixLength, boolean justPrintableSequence) {
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printableSequence = removePrefix(printableSequence, prefixLength);
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if ( !justPrintableSequence )
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actualSequence = removePrefix(actualSequence, prefixLength);
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}
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private static byte[] removePrefix(byte[] sequence, int prefixLength) {
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int newLength = sequence.length - prefixLength;
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byte[] newSequence = new byte[newLength];
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System.arraycopy(sequence, prefixLength, newSequence, 0, newLength);
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return newSequence;
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}
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public void removeSuffix(int suffixLength, boolean justPrintableSequence) {
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printableSequence = removeSuffix(printableSequence, suffixLength);
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if ( !justPrintableSequence )
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actualSequence = removeSuffix(actualSequence, suffixLength);
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}
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private static byte[] removeSuffix(byte[] sequence, int suffixLength) {
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int newLength = sequence.length - suffixLength;
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byte[] newSequence = new byte[newLength];
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System.arraycopy(sequence, 0, newSequence, 0, newLength);
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return newSequence;
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}
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}
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@ -25,22 +25,15 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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// minimum clipped sequence length to consider using
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private static final int MIN_SEQUENCE_LENGTH = 30;
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// minimum multiplicity to consider using
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// private static final int MIN_MULTIPLICITY_TO_USE = 2;
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// FOR DEBUGGING
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private int numReadsToUse = -1;
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// the deBruijn graph object
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private DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> graph = null;
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// simple node class for storing kmer sequences
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protected class DeBruijnVertex {
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protected byte[] sequence;
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public DeBruijnVertex(byte[] sequence) {
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this.sequence = sequence;
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}
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public boolean equals(DeBruijnVertex v) {
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return Arrays.equals(sequence, v.sequence);
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}
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}
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// simple edge class for connecting nodes in the graph
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protected class DeBruijnEdge {
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private int multiplicity;
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@ -59,8 +52,9 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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}
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public SimpleDeBruijnAssembler(PrintStream out, IndexedFastaSequenceFile referenceReader) {
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public SimpleDeBruijnAssembler(PrintStream out, IndexedFastaSequenceFile referenceReader, int numReadsToUse) {
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super(out, referenceReader);
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this.numReadsToUse = numReadsToUse;
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}
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public void runLocalAssembly(List<SAMRecord> reads) {
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@ -84,7 +78,16 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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private List<byte[]> clipReads(List<SAMRecord> reads) {
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List<byte[]> sequences = new ArrayList<byte[]>(reads.size());
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int counter = 0;
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for ( SAMRecord read : reads ) {
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// for debugging
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if ( numReadsToUse >= 0 && ++counter > numReadsToUse ) {
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System.out.println("Stopping before read: " + read.getReadName() + " at " + read.getAlignmentStart());
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break;
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}
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byte[] sequencedReadBases = read.getReadBases();
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byte[] sequencedBaseQuals = read.getBaseQualities();
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@ -165,6 +168,10 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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// create the graph
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createGraphFromSequences(reads);
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// remove nodes with incoming multiplicity of N
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// if ( MIN_MULTIPLICITY_TO_USE > 0 )
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// removeNodesWithLowMultiplicity();
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// cleanup graph by merging nodes
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concatenateNodes();
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@ -176,6 +183,7 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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}
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private void createGraphFromSequences(List<byte[]> reads) {
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for ( byte[] sequence : reads ) {
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final int kmersInSequence = sequence.length - KMER_LENGTH + 1;
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@ -214,8 +222,8 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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}
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private DeBruijnVertex addToGraphIfNew(byte[] kmer) {
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// the graph.containsVertex() method is busted, so here's a hack around it
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// the graph.containsVertex() method is busted, so here's a hack around it
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DeBruijnVertex newV = new DeBruijnVertex(kmer);
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for ( DeBruijnVertex v : graph.vertexSet() ) {
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if ( v.equals(newV) )
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@ -275,10 +283,10 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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// (Vx -> V12 -> Vy)
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// create V12
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int additionalSequenceFromV2 = V2.sequence.length - KMER_LENGTH + 1;
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byte[] newKmer = new byte[V1.sequence.length + additionalSequenceFromV2];
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System.arraycopy(V1.sequence, 0, newKmer, 0, V1.sequence.length);
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System.arraycopy(V2.sequence, KMER_LENGTH - 1, newKmer, V1.sequence.length, additionalSequenceFromV2);
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int additionalSequenceFromV2 = V2.actualSequence.length - KMER_LENGTH + 1;
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byte[] newKmer = new byte[V1.actualSequence.length + additionalSequenceFromV2];
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System.arraycopy(V1.actualSequence, 0, newKmer, 0, V1.actualSequence.length);
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System.arraycopy(V2.actualSequence, KMER_LENGTH - 1, newKmer, V1.actualSequence.length, additionalSequenceFromV2);
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DeBruijnVertex V12 = new DeBruijnVertex(newKmer);
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graph.addVertex(V12);
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@ -307,22 +315,34 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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private void cleanupNodeSequences() {
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// remove the first k-1 bases of the kmers
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for ( DeBruijnVertex v : graph.vertexSet() ) {
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// remove the first k-1 bases of the kmers
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if ( graph.inDegreeOf(v) > 0 )
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removeKmerPrefix(v);
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// move common suffixes from incoming nodes to this one
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if ( graph.inDegreeOf(v) > 1 ) {
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Set<DeBruijnVertex> connectedVs = new HashSet<DeBruijnVertex>();
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for ( DeBruijnEdge edge : graph.incomingEdgesOf(v) )
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connectedVs.add(graph.getEdgeSource(edge));
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propagateCommonSuffix(v, connectedVs);
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}
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v.removePrefix(KMER_LENGTH - 1, true);
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}
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removeEmptyNodes();
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// move common suffixes from incoming nodes to this one
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while ( true ) {
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boolean graphWasModified = false;
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for ( DeBruijnVertex v : graph.vertexSet() ) {
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if ( graph.inDegreeOf(v) > 1 ) {
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Set<DeBruijnVertex> connectedVs = new HashSet<DeBruijnVertex>();
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for ( DeBruijnEdge edge : graph.incomingEdgesOf(v) )
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connectedVs.add(graph.getEdgeSource(edge));
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if ( propagateCommonSuffix(v, connectedVs) ) {
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removeEmptyNodes();
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graphWasModified = true;
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break;
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}
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}
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}
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if ( !graphWasModified )
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break;
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}
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}
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private void removeEmptyNodes() {
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@ -332,26 +352,8 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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boolean graphWasModified = false;
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for ( DeBruijnVertex v : graph.vertexSet() ) {
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if ( v.sequence.length == 0 ) {
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Set<DeBruijnEdge> incoming = graph.incomingEdgesOf(v);
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Set<DeBruijnEdge> outgoing = graph.outgoingEdgesOf(v);
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// make edges from all incoming nodes to all outgoing nodes
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for ( DeBruijnEdge Ex : incoming ) {
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DeBruijnVertex Vx = graph.getEdgeSource(Ex);
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for ( DeBruijnEdge Ey : outgoing ) {
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DeBruijnVertex Vy = graph.getEdgeTarget(Ey);
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DeBruijnEdge newEdge = new DeBruijnEdge();
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newEdge.setMultiplicity(Ex.getMultiplicity());
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graph.addEdge(Vx, Vy, newEdge);
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}
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}
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// remove v and its associated edges
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graph.removeVertex(v);
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if ( v.printableSequence.length == 0 ) {
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removeNode(v);
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graphWasModified = true;
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break;
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}
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@ -362,28 +364,41 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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}
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}
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private void removeKmerPrefix(DeBruijnVertex v) {
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int newLength = v.sequence.length - KMER_LENGTH + 1;
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byte[] newSequence = new byte[newLength];
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System.arraycopy(v.sequence, KMER_LENGTH - 1, newSequence, 0, newLength);
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v.sequence = newSequence;
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private void removeNode(DeBruijnVertex v) {
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Set<DeBruijnEdge> incoming = graph.incomingEdgesOf(v);
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Set<DeBruijnEdge> outgoing = graph.outgoingEdgesOf(v);
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// make edges from all incoming nodes to all outgoing nodes
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for ( DeBruijnEdge Ex : incoming ) {
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DeBruijnVertex Vx = graph.getEdgeSource(Ex);
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for ( DeBruijnEdge Ey : outgoing ) {
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DeBruijnVertex Vy = graph.getEdgeTarget(Ey);
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DeBruijnEdge newEdge = new DeBruijnEdge();
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newEdge.setMultiplicity(Ex.getMultiplicity());
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graph.addEdge(Vx, Vy, newEdge);
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}
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}
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// remove v and its associated edges
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graph.removeVertex(v);
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}
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private void propagateCommonSuffix(DeBruijnVertex Vx, Set<DeBruijnVertex> incoming) {
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private boolean propagateCommonSuffix(DeBruijnVertex Vx, Set<DeBruijnVertex> incoming) {
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// find the common matching suffix
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byte[] match = null;
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for ( DeBruijnVertex v : incoming ) {
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if ( match == null ) {
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match = v.sequence;
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match = v.printableSequence;
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} else {
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int idx = 0;
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while ( idx < match.length && idx < v.sequence.length && match[match.length - idx - 1] == v.sequence[v.sequence.length - idx - 1] )
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while ( idx < match.length && idx < v.printableSequence.length && match[match.length - idx - 1] == v.printableSequence[v.printableSequence.length - idx - 1] )
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idx++;
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if ( idx < match.length ) {
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match = new byte[idx];
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System.arraycopy(v.sequence, v.sequence.length - idx, match, 0, idx);
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System.arraycopy(v.printableSequence, v.printableSequence.length - idx, match, 0, idx);
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}
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}
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}
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@ -391,28 +406,24 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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// if there is a common suffix...
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if ( match != null && match.length > 0 ) {
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// remove it from the end of the incoming nodes
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for ( DeBruijnVertex v : incoming ) {
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int newLength = v.sequence.length - match.length;
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byte[] newSequence = new byte[newLength];
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System.arraycopy(v.sequence, 0, newSequence, 0, newLength);
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v.sequence = newSequence;
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}
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// remove the suffix from the end of the incoming nodes...
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for ( DeBruijnVertex v : incoming )
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v.removeSuffix(match.length, false);
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// and put it at the front of this node
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byte[] newSequence = new byte[Vx.sequence.length + match.length];
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System.arraycopy(match, 0, newSequence, 0, match.length);
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System.arraycopy(Vx.sequence, 0, newSequence, match.length, Vx.sequence.length);
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Vx.sequence = newSequence;
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// ...and put it at the front of this node
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Vx.addPrefix(match, false);
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return true;
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}
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return false;
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}
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private void printGraph() {
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for ( DeBruijnVertex source : graph.vertexSet() ) {
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getOutputStream().print(new String(source.sequence) + " -> ");
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getOutputStream().print(source + " -> ");
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for ( DeBruijnEdge edge : graph.outgoingEdgesOf(source) ) {
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getOutputStream().print(new String(graph.getEdgeTarget(edge).sequence) + " (" + edge.getMultiplicity() + "), ");
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getOutputStream().print(graph.getEdgeTarget(edge) + " (" + edge.getMultiplicity() + "), ");
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}
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getOutputStream().println();
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}
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@ -424,4 +435,21 @@ public class SimpleDeBruijnAssembler extends LocalAssemblyEngine {
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// TODO -- implement me
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}
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/****
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private void removeNodesWithLowMultiplicity() {
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Set<DeBruijnVertex> vertexSet = graph.vertexSet();
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// convert to array because results of the iteration on a set are undefined when the graph is modified
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ArrayList<DeBruijnVertex> vertices = new ArrayList<DeBruijnVertex>(vertexSet);
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for (int i = 0; i < vertices.size(); i++) {
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DeBruijnVertex v = vertices.get(i);
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if ( graph.inDegreeOf(v) == 1 &&
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graph.incomingEdgesOf(v).iterator().next().getMultiplicity() < MIN_MULTIPLICITY_TO_USE )
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removeNode(v);
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}
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}
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****/
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}
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.assembly;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import net.sf.samtools.*;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Hidden;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
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@ -53,6 +54,10 @@ public class WindowedAssemblyWalker extends ReadWalker<SAMRecord, Integer> {
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@Argument(fullName = "assembler", shortName = "assembler", doc = "Assembler to use; currently only SIMPLE_DE_BRUIJN is available.", required = false)
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protected LocalAssemblyEngine.ASSEMBLER ASSEMBLER_TO_USE = LocalAssemblyEngine.ASSEMBLER.SIMPLE_DE_BRUIJN;
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@Hidden
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@Argument(fullName = "readsToUse", shortName = "readsToUse", doc = "For debugging: how many reads to use")
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protected int numReadsToUse = -1;
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// the assembly engine
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LocalAssemblyEngine assemblyEngine = null;
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@ -90,7 +95,7 @@ public class WindowedAssemblyWalker extends ReadWalker<SAMRecord, Integer> {
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private LocalAssemblyEngine makeAssembler(LocalAssemblyEngine.ASSEMBLER type, IndexedFastaSequenceFile referenceReader) {
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switch ( type ) {
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case SIMPLE_DE_BRUIJN:
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return new SimpleDeBruijnAssembler(graphWriter, referenceReader);
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return new SimpleDeBruijnAssembler(graphWriter, referenceReader, numReadsToUse);
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default:
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throw new UserException.BadInput("Assembler type " + type + " is not valid/supported");
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}
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