Basic kmer error correction algorithm xfor the HaplotypeCaller
-- Error correction algorithm for the assembler. Only error correct reads to others that are exactly 1 mismatch away -- The assembler logic is now: build initial graph, error correct*, merge nodes*, prune dead nodes, merge again, make haplotypes. The * elements are new -- Refactored the printing routines a bit so it's easy to write a single graph to disk for testing. -- Easier way to control the testing of the graph assembly algorithms -- Move graph printing function to DeBruijnAssemblyGraph from DeBruijnAssembler -- Simple protected parsing function for making DeBruijnAssemblyGraph -- Change the default prune factor for the graph to 1, from 2 -- debugging graph transformations are controllable from command line
This commit is contained in:
Mark DePristo
parent
53a904bcbd
commit
0f4328f6fe
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@ -64,6 +64,9 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.broadinstitute.variant.variantcontext.Allele;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.PrintStream;
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import java.util.*;
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@ -88,16 +91,19 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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private static final double SW_GAP_EXTEND = -1.2; //-1.0/.0;
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private final boolean debug;
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private final int onlyBuildKmerGraphOfThisSite = -1; // 35;
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private final boolean debugGraphTransformations;
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private final PrintStream graphWriter;
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private final List<DeBruijnAssemblyGraph> graphs = new ArrayList<DeBruijnAssemblyGraph>();
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private final int minKmer;
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private final int maxHaplotypesToConsider;
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private int PRUNE_FACTOR = 2;
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public DeBruijnAssembler(final boolean debug, final PrintStream graphWriter, final int minKmer, final int maxHaplotypesToConsider) {
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public DeBruijnAssembler(final boolean debug, final boolean debugGraphTransformations, final PrintStream graphWriter, final int minKmer, final int maxHaplotypesToConsider) {
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super();
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this.debug = debug;
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this.debugGraphTransformations = debugGraphTransformations;
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this.graphWriter = graphWriter;
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this.minKmer = minKmer;
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this.maxHaplotypesToConsider = maxHaplotypesToConsider;
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@ -144,13 +150,23 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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// create the graph for each possible kmer
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for( int kmer = maxKmer; kmer >= minKmer; kmer -= GRAPH_KMER_STEP ) {
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//if ( debug ) logger.info("Creating de Bruijn graph for " + kmer + " kmer using " + reads.size() + " reads");
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final DeBruijnAssemblyGraph graph = createGraphFromSequences( reads, kmer, refHaplotype, debug);
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if ( onlyBuildKmerGraphOfThisSite != -1 && kmer != onlyBuildKmerGraphOfThisSite )
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continue;
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if ( debug ) logger.info("Creating de Bruijn graph for " + kmer + " kmer using " + reads.size() + " reads");
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DeBruijnAssemblyGraph graph = createGraphFromSequences( reads, kmer, refHaplotype, debug);
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if( graph != null ) { // graphs that fail during creation ( for example, because there are cycles in the reference graph ) will show up here as a null graph object
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// do a series of steps to clean up the raw assembly graph to make it analysis-ready
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pruneGraph(graph, PRUNE_FACTOR);
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if ( debugGraphTransformations ) graph.printGraph(new File("unpruned.dot"), PRUNE_FACTOR);
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graph = graph.errorCorrect();
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if ( debugGraphTransformations ) graph.printGraph(new File("errorCorrected.dot"), PRUNE_FACTOR);
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cleanNonRefPaths(graph);
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mergeNodes(graph);
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if ( debugGraphTransformations ) graph.printGraph(new File("merged.dot"), PRUNE_FACTOR);
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pruneGraph(graph, PRUNE_FACTOR);
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if ( debugGraphTransformations ) graph.printGraph(new File("pruned.dot"), PRUNE_FACTOR);
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mergeNodes(graph);
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if ( debugGraphTransformations ) graph.printGraph(new File("merged2.dot"), PRUNE_FACTOR);
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if( graph.getReferenceSourceVertex() != null ) { // if the graph contains interesting variation from the reference
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sanityCheckReferenceGraph(graph, refHaplotype);
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graphs.add(graph);
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@ -169,7 +185,7 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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final DeBruijnVertex outgoingVertex = graph.getEdgeTarget(e);
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final DeBruijnVertex incomingVertex = graph.getEdgeSource(e);
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if( !outgoingVertex.equals(incomingVertex) && graph.outDegreeOf(incomingVertex) == 1 && graph.inDegreeOf(outgoingVertex) == 1 &&
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graph.inDegreeOf(incomingVertex) <= 1 && graph.outDegreeOf(outgoingVertex) <= 1 && graph.isReferenceNode(incomingVertex) == graph.isReferenceNode(outgoingVertex) ) {
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graph.inDegreeOf(incomingVertex) <= 1 && graph.outDegreeOf(outgoingVertex) <= 1 && graph.isReferenceNode(incomingVertex) == graph.isReferenceNode(outgoingVertex) ) {
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final Set<DeBruijnEdge> outEdges = graph.outgoingEdgesOf(outgoingVertex);
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final Set<DeBruijnEdge> inEdges = graph.incomingEdgesOf(incomingVertex);
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if( inEdges.size() == 1 && outEdges.size() == 1 ) {
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@ -199,6 +215,59 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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}
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}
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//
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// X -> ABC -> Y
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// -> aBC -> Y
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//
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// becomes
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//
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// X -> A -> BCY
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// -> a -> BCY
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//
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// @Requires({"graph != null"})
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// protected static void simplifyMergedGraph(final DeBruijnAssemblyGraph graph) {
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// boolean foundNodesToMerge = true;
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// while( foundNodesToMerge ) {
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// foundNodesToMerge = false;
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//
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// for( final DeBruijnVertex v : graph.vertexSet() ) {
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// if ( isRootOfComplexDiamond(v) ) {
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// foundNodesToMerge = simplifyComplexDiamond(graph, v);
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// if ( foundNodesToMerge )
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// break;
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// }
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// }
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// }
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// }
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//
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// private static boolean simplifyComplexDiamond(final DeBruijnAssemblyGraph graph, final DeBruijnVertex root) {
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// final Set<DeBruijnEdge> outEdges = graph.outgoingEdgesOf(root);
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// final DeBruijnVertex diamondBottom = graph.getEdge(graph.getEdgeTarget(outEdges.iterator().next());
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// // all of the edges point to the same sink, so it's time to merge
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// final byte[] commonSuffix = commonSuffixOfEdgeTargets(outEdges, targetSink);
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// if ( commonSuffix != null ) {
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// final DeBruijnVertex suffixVertex = new DeBruijnVertex(commonSuffix, graph.getKmerSize());
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// graph.addVertex(suffixVertex);
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// graph.addEdge(suffixVertex, targetSink);
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//
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// for( final DeBruijnEdge edge : outEdges ) {
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// final DeBruijnVertex target = graph.getEdgeTarget(edge);
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// final DeBruijnVertex prefix = target.withoutSuffix(commonSuffix);
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// graph.addEdge(prefix, suffixVertex, new DeBruijnEdge(edge.isRef(), edge.getMultiplicity()));
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// graph.removeVertex(graph.getEdgeTarget(edge));
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// graph.removeAllEdges(root, target);
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// graph.removeAllEdges(target, targetSink);
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// }
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//
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// graph.removeAllEdges(outEdges);
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// graph.removeVertex(targetSink);
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//
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// return true;
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// } else {
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// return false;
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// }
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// }
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protected static void cleanNonRefPaths( final DeBruijnAssemblyGraph graph ) {
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if( graph.getReferenceSourceVertex() == null || graph.getReferenceSinkVertex() == null ) {
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return;
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@ -279,7 +348,7 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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if( refSequence.length >= KMER_LENGTH + KMER_OVERLAP ) {
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final int kmersInSequence = refSequence.length - KMER_LENGTH + 1;
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for( int iii = 0; iii < kmersInSequence - 1; iii++ ) {
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if( !graph.addKmersToGraph(Arrays.copyOfRange(refSequence, iii, iii + KMER_LENGTH), Arrays.copyOfRange(refSequence, iii + 1, iii + 1 + KMER_LENGTH), true) ) {
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if( !graph.addKmersToGraph(Arrays.copyOfRange(refSequence, iii, iii + KMER_LENGTH), Arrays.copyOfRange(refSequence, iii + 1, iii + 1 + KMER_LENGTH), true, 1) ) {
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if( DEBUG ) {
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System.out.println("Cycle detected in reference graph for kmer = " + KMER_LENGTH + " ...skipping");
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}
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@ -297,7 +366,7 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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final byte[] reducedReadCounts = read.getReducedReadCounts(); // will be null if read is not reduced
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if( sequence.length > KMER_LENGTH + KMER_OVERLAP ) {
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final int kmersInSequence = sequence.length - KMER_LENGTH + 1;
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for( int iii = 0; iii < kmersInSequence - 1; iii++ ) {
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for( int iii = 0; iii < kmersInSequence - 1; iii++ ) {
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// if the qualities of all the bases in the kmers are high enough
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boolean badKmer = false;
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for( int jjj = iii; jjj < iii + KMER_LENGTH + 1; jjj++) {
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@ -318,42 +387,32 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
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final byte[] kmer2 = Arrays.copyOfRange(sequence, iii + 1, iii + 1 + KMER_LENGTH);
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for( int kkk=0; kkk < countNumber; kkk++ ) {
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graph.addKmersToGraph(kmer1, kmer2, false);
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graph.addKmersToGraph(kmer1, kmer2, false, 1);
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}
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}
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}
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}
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}
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return graph;
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}
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protected void printGraphs() {
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final boolean onlyWriteOneGraph = false; // debugging flag -- if true we'll only write a graph for a single kmer size
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final int writeFirstGraphWithSizeSmallerThan = 50;
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graphWriter.println("digraph assemblyGraphs {");
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for( final DeBruijnAssemblyGraph graph : graphs ) {
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if ( onlyWriteOneGraph && graph.getKmerSize() >= writeFirstGraphWithSizeSmallerThan ) {
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if ( debugGraphTransformations && graph.getKmerSize() >= writeFirstGraphWithSizeSmallerThan ) {
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logger.info("Skipping writing of graph with kmersize " + graph.getKmerSize());
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continue;
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}
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for( final DeBruijnEdge edge : graph.edgeSet() ) {
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if( edge.getMultiplicity() > PRUNE_FACTOR ) {
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graphWriter.println("\t" + graph.getEdgeSource(edge).toString() + " -> " + graph.getEdgeTarget(edge).toString() + " [" + (edge.getMultiplicity() <= PRUNE_FACTOR ? "style=dotted,color=grey" : "label=\"" + edge.getMultiplicity() + "\"") + "];");
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}
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if( edge.isRef() ) {
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graphWriter.println("\t" + graph.getEdgeSource(edge).toString() + " -> " + graph.getEdgeTarget(edge).toString() + " [color=red];");
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}
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if( !edge.isRef() && edge.getMultiplicity() <= PRUNE_FACTOR ) { System.out.println("Graph pruning warning!"); }
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}
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for( final DeBruijnVertex v : graph.vertexSet() ) {
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graphWriter.println("\t" + v.toString() + " [label=\"" + new String(graph.getAdditionalSequence(v)) + "\",shape=box]");
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}
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graph.printGraph(graphWriter, false, PRUNE_FACTOR);
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if ( onlyWriteOneGraph )
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if ( debugGraphTransformations )
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break;
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}
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graphWriter.println("}");
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}
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@ -48,8 +48,12 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
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import com.google.java.contract.Ensures;
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import org.apache.commons.lang.ArrayUtils;
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import org.apache.log4j.Logger;
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import org.jgrapht.graph.DefaultDirectedGraph;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.PrintStream;
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import java.util.Arrays;
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@ -60,6 +64,7 @@ import java.util.Arrays;
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*/
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public class DeBruijnAssemblyGraph extends DefaultDirectedGraph<DeBruijnVertex, DeBruijnEdge> {
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private final static Logger logger = Logger.getLogger(DeBruijnAssemblyGraph.class);
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private final int kmerSize;
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/**
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@ -73,6 +78,24 @@ public class DeBruijnAssemblyGraph extends DefaultDirectedGraph<DeBruijnVertex,
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this.kmerSize = kmerSize;
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}
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public static DeBruijnAssemblyGraph parse(final int kmerSize, final int multiplicity, final String ... reads) {
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final DeBruijnAssemblyGraph graph = new DeBruijnAssemblyGraph(kmerSize);
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for ( final String read : reads ) {
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final int kmersInSequence = read.length() - kmerSize + 1;
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for (int i = 0; i < kmersInSequence - 1; i++) {
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// get the kmers
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final byte[] kmer1 = new byte[kmerSize];
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System.arraycopy(read.getBytes(), i, kmer1, 0, kmerSize);
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final byte[] kmer2 = new byte[kmerSize];
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System.arraycopy(read.getBytes(), i+1, kmer2, 0, kmerSize);
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graph.addKmersToGraph(kmer1, kmer2, false, multiplicity);
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}
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}
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return graph;
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}
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/**
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* Test construct that makes DeBruijnAssemblyGraph assuming a kmerSize of 11
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*/
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@ -102,13 +125,22 @@ public class DeBruijnAssemblyGraph extends DefaultDirectedGraph<DeBruijnVertex,
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/**
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* @param v the vertex to test
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* @return true if this vertex is a source node
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* @return true if this vertex is a source node (in degree == 0)
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*/
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public boolean isSource( final DeBruijnVertex v ) {
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if( v == null ) { throw new IllegalArgumentException("Attempting to test a null vertex."); }
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return inDegreeOf(v) == 0;
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}
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/**
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* @param v the vertex to test
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* @return true if this vertex is a sink node (out degree == 0)
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*/
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public boolean isSink( final DeBruijnVertex v ) {
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if( v == null ) { throw new IllegalArgumentException("Attempting to test a null vertex."); }
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return outDegreeOf(v) == 0;
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}
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/**
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* Pull out the additional sequence implied by traversing this node in the graph
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* @param v the vertex from which to pull out the additional base sequence
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@ -284,10 +316,36 @@ public class DeBruijnAssemblyGraph extends DefaultDirectedGraph<DeBruijnVertex,
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if( sequence.length < KMER_LENGTH + 1 ) { throw new IllegalArgumentException("Provided sequence is too small for the given kmer length"); }
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final int kmersInSequence = sequence.length - KMER_LENGTH + 1;
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for( int iii = 0; iii < kmersInSequence - 1; iii++ ) {
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addKmersToGraph(Arrays.copyOfRange(sequence, iii, iii + KMER_LENGTH), Arrays.copyOfRange(sequence, iii + 1, iii + 1 + KMER_LENGTH), isRef);
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addKmersToGraph(Arrays.copyOfRange(sequence, iii, iii + KMER_LENGTH), Arrays.copyOfRange(sequence, iii + 1, iii + 1 + KMER_LENGTH), isRef, 1);
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}
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}
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protected DeBruijnAssemblyGraph errorCorrect() {
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final KMerErrorCorrector corrector = new KMerErrorCorrector(getKmerSize(), 1, 1, 5); // TODO -- should be static variables
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for( final DeBruijnEdge e : edgeSet() ) {
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for ( final byte[] kmer : Arrays.asList(getEdgeSource(e).getSequence(), getEdgeTarget(e).getSequence())) {
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// TODO -- need a cleaner way to deal with the ref weight
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corrector.addKmer(kmer, e.isRef() ? 1000 : e.getMultiplicity());
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}
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}
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corrector.computeErrorCorrectionMap();
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//logger.info(corrector);
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final DeBruijnAssemblyGraph correctedGraph = new DeBruijnAssemblyGraph(getKmerSize());
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for( final DeBruijnEdge e : edgeSet() ) {
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final byte[] source = corrector.getErrorCorrectedKmer(getEdgeSource(e).getSequence());
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final byte[] target = corrector.getErrorCorrectedKmer(getEdgeTarget(e).getSequence());
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if ( source != null && target != null ) {
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correctedGraph.addKmersToGraph(source, target, e.isRef(), e.getMultiplicity());
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}
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}
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return correctedGraph;
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}
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/**
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* Add edge to assembly graph connecting the two kmers
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* @param kmer1 the source kmer for the edge
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@ -295,7 +353,7 @@ public class DeBruijnAssemblyGraph extends DefaultDirectedGraph<DeBruijnVertex,
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* @param isRef true if the added edge is a reference edge
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* @return will return false if trying to add a reference edge which creates a cycle in the assembly graph
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*/
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public boolean addKmersToGraph( final byte[] kmer1, final byte[] kmer2, final boolean isRef ) {
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public boolean addKmersToGraph( final byte[] kmer1, final byte[] kmer2, final boolean isRef, final int multiplicity ) {
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if( kmer1 == null ) { throw new IllegalArgumentException("Attempting to add a null kmer to the graph."); }
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if( kmer2 == null ) { throw new IllegalArgumentException("Attempting to add a null kmer to the graph."); }
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if( kmer1.length != kmer2.length ) { throw new IllegalArgumentException("Attempting to add a kmers to the graph with different lengths."); }
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@ -309,34 +367,61 @@ public class DeBruijnAssemblyGraph extends DefaultDirectedGraph<DeBruijnVertex,
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final DeBruijnEdge targetEdge = getEdge(v1, v2);
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if ( targetEdge == null ) {
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addEdge(v1, v2, new DeBruijnEdge( isRef ));
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addEdge(v1, v2, new DeBruijnEdge( isRef, multiplicity ));
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} else {
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if( isRef ) {
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targetEdge.setIsRef( true );
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}
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targetEdge.setMultiplicity(targetEdge.getMultiplicity() + 1);
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targetEdge.setMultiplicity(targetEdge.getMultiplicity() + multiplicity);
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}
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return true;
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}
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/**
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* Print out the graph in the dot language for visualization
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* @param GRAPH_WRITER PrintStream to write to
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* Convenience function to add multiple vertices to the graph at once
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* @param vertices one or more vertices to add
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*/
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public void printGraph( final PrintStream GRAPH_WRITER ) {
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if( GRAPH_WRITER == null ) { throw new IllegalArgumentException("PrintStream cannot be null."); }
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public void addVertices(final DeBruijnVertex ... vertices) {
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for ( final DeBruijnVertex v : vertices )
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addVertex(v);
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}
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/**
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* Print out the graph in the dot language for visualization
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* @param destination File to write to
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*/
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public void printGraph(final File destination, final int pruneFactor) {
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PrintStream stream = null;
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try {
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stream = new PrintStream(new FileOutputStream(destination));
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printGraph(stream, true, pruneFactor);
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} catch ( FileNotFoundException e ) {
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throw new RuntimeException(e);
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} finally {
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if ( stream != null ) stream.close();
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}
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}
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public void printGraph(final PrintStream graphWriter, final boolean writeHeader, final int pruneFactor) {
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if ( writeHeader )
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graphWriter.println("digraph assemblyGraphs {");
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GRAPH_WRITER.println("digraph assembly {");
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for( final DeBruijnEdge edge : edgeSet() ) {
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GRAPH_WRITER.println("\t" + getEdgeSource(edge).toString() + " -> " + getEdgeTarget(edge).toString() + " [" + "label=\""+ edge.getMultiplicity() +"\"" + "];");
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// if( edge.getMultiplicity() > PRUNE_FACTOR ) {
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graphWriter.println("\t" + getEdgeSource(edge).toString() + " -> " + getEdgeTarget(edge).toString() + " [" + (edge.getMultiplicity() <= pruneFactor ? "style=dotted,color=grey," : "") + "label=\"" + edge.getMultiplicity() + "\"];");
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// }
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if( edge.isRef() ) {
|
||||
GRAPH_WRITER.println("\t" + getEdgeSource(edge).toString() + " -> " + getEdgeTarget(edge).toString() + " [color=red];");
|
||||
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 DeBruijnVertex v : vertexSet() ) {
|
||||
final String label = ( inDegreeOf(v) == 0 ? v.toString() : v.getSuffixString() );
|
||||
GRAPH_WRITER.println("\t" + v.toString() + " [label=\"" + label + "\"]");
|
||||
graphWriter.println("\t" + v.toString() + " [label=\"" + new String(getAdditionalSequence(v)) + "\",shape=box]");
|
||||
}
|
||||
GRAPH_WRITER.println("}");
|
||||
|
||||
if ( writeHeader )
|
||||
graphWriter.println("}");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -68,6 +68,18 @@ public class DeBruijnVertex {
|
|||
this.kmer = kmer;
|
||||
}
|
||||
|
||||
protected DeBruijnVertex( final String sequence, final int kmer ) {
|
||||
this(sequence.getBytes(), kmer);
|
||||
}
|
||||
|
||||
protected DeBruijnVertex( final String sequence ) {
|
||||
this(sequence.getBytes(), sequence.length());
|
||||
}
|
||||
|
||||
public int getKmer() {
|
||||
return kmer;
|
||||
}
|
||||
|
||||
@Override
|
||||
public boolean equals( Object v ) {
|
||||
return v instanceof DeBruijnVertex && Arrays.equals(sequence, ((DeBruijnVertex) v).sequence);
|
||||
|
|
|
|||
|
|
@ -192,7 +192,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
|
|||
protected String keepRG = null;
|
||||
|
||||
@Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with <= X supporting kmers are pruned from the graph", required = false)
|
||||
protected int MIN_PRUNE_FACTOR = 2;
|
||||
protected int MIN_PRUNE_FACTOR = 1;
|
||||
|
||||
@Advanced
|
||||
@Argument(fullName="gcpHMM", shortName="gcpHMM", doc="Flat gap continuation penalty for use in the Pair HMM", required = false)
|
||||
|
|
@ -284,6 +284,9 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
|
|||
@Argument(fullName="debug", shortName="debug", doc="If specified, print out very verbose debug information about each triggering active region", required = false)
|
||||
protected boolean DEBUG;
|
||||
|
||||
@Argument(fullName="debugGraphTransformations", shortName="debugGraphTransformations", doc="If specified, we will write DOT formatted graph files out of the assembler", required = false)
|
||||
protected boolean debugGraphTransformations = false;
|
||||
|
||||
// the UG engines
|
||||
private UnifiedGenotyperEngine UG_engine = null;
|
||||
private UnifiedGenotyperEngine UG_engine_simple_genotyper = null;
|
||||
|
|
@ -386,7 +389,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
|
|||
throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile, e);
|
||||
}
|
||||
|
||||
assemblyEngine = new DeBruijnAssembler( DEBUG, graphWriter, minKmer, maxHaplotypesToConsider );
|
||||
assemblyEngine = new DeBruijnAssembler( DEBUG, debugGraphTransformations, graphWriter, minKmer, maxHaplotypesToConsider );
|
||||
likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
|
||||
genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS );
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,253 @@
|
|||
/*
|
||||
* 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 java.util.*;
|
||||
|
||||
/**
|
||||
* generic utility function that error corrects kmers based on counts
|
||||
*
|
||||
* This class provides a generic facility for remapping kmers (byte[] of constant size)
|
||||
* that occur infrequently to those that occur frequently, based on their simple edit distance
|
||||
* as measured by mismatches.
|
||||
*
|
||||
* The overall workflow of using this class is simple. First, you create the class with
|
||||
* parameters determining how the error correction should proceed. Next, you provide all
|
||||
* of the kmers you see in your data. Once all kmers have been added, you call computeErrorCorrectionMap
|
||||
* to tell this class that all kmers have been added and its time to determine error correcting
|
||||
* mapping from observed kmers to corrected kmers. This correction looks for low-count (as determined
|
||||
* by maxCountToCorrect) kmers and chooses the best kmer (minimizing mismatches) among those
|
||||
* with at least minCountOfKmerToBeCorrection occurrences to error correct the kmer to. If
|
||||
* there is no kmer with less than maxMismatchesToCorrect then the kmer will be mapped to
|
||||
* null, indicating the kmer should not be used.
|
||||
*
|
||||
* TODO -- for ease of implementation this class uses strings instead of byte[] as those cannot
|
||||
* TODO -- be added to hashmaps (more specifically, those don't implement .equals). A more efficient
|
||||
* TODO -- version would use the byte[] directly
|
||||
*
|
||||
* User: depristo
|
||||
* Date: 3/8/13
|
||||
* Time: 1:16 PM
|
||||
*/
|
||||
public class KMerErrorCorrector {
|
||||
/**
|
||||
* A map of for each kmer to its num occurrences in addKmers
|
||||
*/
|
||||
Map<String, Integer> countsByKMer = new HashMap<String, Integer>();
|
||||
|
||||
/**
|
||||
* A map from raw kmer -> error corrected kmer
|
||||
*/
|
||||
Map<String, String> rawToErrorCorrectedMap = null;
|
||||
|
||||
final int kmerLength;
|
||||
final int maxCountToCorrect;
|
||||
final int maxMismatchesToCorrect;
|
||||
final int minCountOfKmerToBeCorrection;
|
||||
|
||||
/**
|
||||
* Create a new kmer corrector
|
||||
*
|
||||
* @param kmerLength the length of kmers we'll be counting to error correct, must be >= 1
|
||||
* @param maxCountToCorrect kmers with < maxCountToCorrect will try to be error corrected to another kmer, must be >= 0
|
||||
* @param maxMismatchesToCorrect the maximum number of mismatches between a to-be-corrected kmer and its
|
||||
* best match that we attempt to error correct. If no sufficiently similar
|
||||
* kmer exists, it will be remapped to null. Must be >= 1
|
||||
* @param minCountOfKmerToBeCorrection the minimum count of a kmer to be considered a target for correction.
|
||||
* That is, kmers that need correction will only be matched with kmers
|
||||
* with at least minCountOfKmerToBeCorrection occurrences. Must be >= 1
|
||||
*/
|
||||
public KMerErrorCorrector(final int kmerLength,
|
||||
final int maxCountToCorrect,
|
||||
final int maxMismatchesToCorrect,
|
||||
final int minCountOfKmerToBeCorrection) {
|
||||
if ( kmerLength < 1 ) throw new IllegalArgumentException("kmerLength must be > 0 but got " + kmerLength);
|
||||
if ( maxCountToCorrect < 0 ) throw new IllegalArgumentException("maxCountToCorrect must be >= 0 but got " + maxCountToCorrect);
|
||||
if ( maxMismatchesToCorrect < 1 ) throw new IllegalArgumentException("maxMismatchesToCorrect must be >= 1 but got " + maxMismatchesToCorrect);
|
||||
if ( minCountOfKmerToBeCorrection < 1 ) throw new IllegalArgumentException("minCountOfKmerToBeCorrection must be >= 1 but got " + minCountOfKmerToBeCorrection);
|
||||
|
||||
this.kmerLength = kmerLength;
|
||||
this.maxCountToCorrect = maxCountToCorrect;
|
||||
this.maxMismatchesToCorrect = maxMismatchesToCorrect;
|
||||
this.minCountOfKmerToBeCorrection = minCountOfKmerToBeCorrection;
|
||||
}
|
||||
|
||||
/**
|
||||
* For testing purposes
|
||||
*
|
||||
* @param kmers
|
||||
*/
|
||||
protected void addKmers(final String ... kmers) {
|
||||
for ( final String kmer : kmers )
|
||||
addKmer(kmer, 1);
|
||||
computeErrorCorrectionMap();
|
||||
}
|
||||
|
||||
/**
|
||||
* Add a kmer that occurred kmerCount times
|
||||
*
|
||||
* @param rawKmer a kmer
|
||||
* @param kmerCount the number of occurrences
|
||||
*/
|
||||
public void addKmer(final byte[] rawKmer, final int kmerCount) {
|
||||
addKmer(new String(rawKmer), kmerCount);
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Get the error corrected kmer for rawKmer
|
||||
*
|
||||
* @param rawKmer a kmer that was already added that we want to get an error corrected version for
|
||||
* @return an error corrected kmer to use instead of rawKmer. May be == rawKmer if no error correction
|
||||
* is not necessary. May be null, indicating the rawKmer shouldn't be used at all
|
||||
*/
|
||||
public byte[] getErrorCorrectedKmer(final byte[] rawKmer) {
|
||||
final String result = getErrorCorrectedKmer(new String(rawKmer));
|
||||
return result == null ? null : result.getBytes();
|
||||
}
|
||||
|
||||
/**
|
||||
* Indicate that no more kmers will be added to the kmer error corrector, so that the
|
||||
* error correction data structure should be computed from the added kmers. Enabled calls
|
||||
* to getErrorCorrectedKmer, and disable calls to addKmer.
|
||||
*/
|
||||
public void computeErrorCorrectionMap() {
|
||||
if ( countsByKMer == null )
|
||||
throw new IllegalStateException("computeErrorCorrectionMap can only be called once");
|
||||
|
||||
final LinkedList<String> needsCorrection = new LinkedList<String>();
|
||||
final LinkedList<String> goodKmers = new LinkedList<String>();
|
||||
|
||||
rawToErrorCorrectedMap = new HashMap<String, String>();
|
||||
for ( Map.Entry<String, Integer> kmerCounts: countsByKMer.entrySet() ) {
|
||||
if ( kmerCounts.getValue() <= maxCountToCorrect )
|
||||
needsCorrection.add(kmerCounts.getKey());
|
||||
else {
|
||||
// todo -- optimization could make not in map mean ==
|
||||
rawToErrorCorrectedMap.put(kmerCounts.getKey(), kmerCounts.getKey());
|
||||
|
||||
// only allow corrections to kmers with at least this count
|
||||
if ( kmerCounts.getValue() >= minCountOfKmerToBeCorrection )
|
||||
goodKmers.add(kmerCounts.getKey());
|
||||
}
|
||||
}
|
||||
|
||||
for ( final String toCorrect : needsCorrection ) {
|
||||
final String corrected = findClosestKMer(toCorrect, goodKmers);
|
||||
rawToErrorCorrectedMap.put(toCorrect, corrected);
|
||||
}
|
||||
|
||||
// cleanup memory -- we don't need the counts for each kmer any longer
|
||||
countsByKMer = null;
|
||||
}
|
||||
|
||||
protected void addKmer(final String rawKmer, final int kmerCount) {
|
||||
if ( rawKmer.length() != kmerLength ) throw new IllegalArgumentException("bad kmer length " + rawKmer + " expected size " + kmerLength);
|
||||
if ( kmerCount < 0 ) throw new IllegalArgumentException("bad kmerCount " + kmerCount);
|
||||
if ( countsByKMer == null ) throw new IllegalStateException("Cannot add kmers to an already finalized error corrector");
|
||||
|
||||
final Integer countFromMap = countsByKMer.get(rawKmer);
|
||||
final int count = countFromMap == null ? 0 : countFromMap;
|
||||
countsByKMer.put(rawKmer, count + kmerCount);
|
||||
}
|
||||
|
||||
protected String findClosestKMer(final String kmer, final Collection<String> goodKmers) {
|
||||
String bestMatch = null;
|
||||
int minMismatches = Integer.MAX_VALUE;
|
||||
|
||||
for ( final String goodKmer : goodKmers ) {
|
||||
final int mismatches = countMismatches(kmer, goodKmer);
|
||||
if ( mismatches < minMismatches ) {
|
||||
minMismatches = mismatches;
|
||||
bestMatch = goodKmer;
|
||||
}
|
||||
}
|
||||
|
||||
return minMismatches > maxMismatchesToCorrect ? null : bestMatch;
|
||||
}
|
||||
|
||||
protected int countMismatches(final String one, final String two) {
|
||||
int mismatches = 0;
|
||||
for ( int i = 0; i < one.length(); i++ )
|
||||
mismatches += one.charAt(i) == two.charAt(i) ? 0 : 1;
|
||||
return mismatches;
|
||||
}
|
||||
|
||||
protected String getErrorCorrectedKmer(final String rawKmer) {
|
||||
if ( rawToErrorCorrectedMap == null ) throw new IllegalStateException("Cannot get error corrected kmers until after computeErrorCorrectionMap has been called");
|
||||
if ( rawKmer.length() != kmerLength ) throw new IllegalArgumentException("bad kmer length " + rawKmer + " expected size " + kmerLength);
|
||||
return rawToErrorCorrectedMap.get(rawKmer);
|
||||
}
|
||||
|
||||
@Override
|
||||
public String toString() {
|
||||
final StringBuilder b = new StringBuilder("KMerErrorCorrector{");
|
||||
for ( Map.Entry<String, String> toCorrect : rawToErrorCorrectedMap.entrySet() ) {
|
||||
final boolean correcting = ! toCorrect.getKey().equals(toCorrect.getValue());
|
||||
if ( correcting )
|
||||
b.append(String.format("%n\t%s / %d -> %s / %d [correcting? %b]",
|
||||
toCorrect.getKey(), getCounts(toCorrect.getKey()),
|
||||
toCorrect.getValue(), getCounts(toCorrect.getValue()),
|
||||
correcting));
|
||||
}
|
||||
b.append("\n}");
|
||||
return b.toString();
|
||||
}
|
||||
|
||||
/**
|
||||
* Get a simple count estimate for printing for kmer
|
||||
* @param kmer the kmer
|
||||
* @return an integer count for kmer
|
||||
*/
|
||||
private int getCounts(final String kmer) {
|
||||
if ( kmer == null ) return 0;
|
||||
final Integer count = countsByKMer == null ? -1 : countsByKMer.get(kmer);
|
||||
if ( count == null )
|
||||
throw new IllegalArgumentException("kmer not found in counts -- bug " + kmer);
|
||||
return count;
|
||||
}
|
||||
}
|
||||
|
|
@ -67,6 +67,7 @@ import org.testng.annotations.Test;
|
|||
import java.util.*;
|
||||
|
||||
public class DeBruijnAssemblerUnitTest extends BaseTest {
|
||||
private final static boolean DEBUG = true;
|
||||
|
||||
|
||||
private class MergeNodesWithNoVariationTestProvider extends TestDataProvider {
|
||||
|
|
@ -97,7 +98,7 @@ public class DeBruijnAssemblerUnitTest extends BaseTest {
|
|||
final byte[] kmer2 = new byte[KMER_LENGTH];
|
||||
System.arraycopy(sequence, i+1, kmer2, 0, KMER_LENGTH);
|
||||
|
||||
graph.addKmersToGraph(kmer1, kmer2, false);
|
||||
graph.addKmersToGraph(kmer1, kmer2, false, 1);
|
||||
}
|
||||
DeBruijnAssembler.mergeNodes(graph);
|
||||
return graph;
|
||||
|
|
@ -118,13 +119,70 @@ public class DeBruijnAssemblerUnitTest extends BaseTest {
|
|||
return MergeNodesWithNoVariationTestProvider.getTests(MergeNodesWithNoVariationTestProvider.class);
|
||||
}
|
||||
|
||||
@Test(dataProvider = "MergeNodesWithNoVariationTestProvider", enabled = true)
|
||||
@Test(dataProvider = "MergeNodesWithNoVariationTestProvider", enabled = !DEBUG)
|
||||
public void testMergeNodesWithNoVariation(MergeNodesWithNoVariationTestProvider cfg) {
|
||||
logger.warn(String.format("Test: %s", cfg.toString()));
|
||||
Assert.assertTrue(graphEquals(cfg.calcGraph(), cfg.expectedGraph()));
|
||||
}
|
||||
|
||||
@Test(enabled = true)
|
||||
// @DataProvider(name = "SimpleMergeOperationsData")
|
||||
// public Object[][] makeSimpleMergeOperationsData() {
|
||||
// List<Object[]> tests = new ArrayList<Object[]>();
|
||||
//
|
||||
// {
|
||||
// DeBruijnAssemblyGraph graph = new DeBruijnAssemblyGraph();
|
||||
// DeBruijnVertex v1 = new DeBruijnVertex("AT");
|
||||
// DeBruijnVertex v2 = new DeBruijnVertex("TC");
|
||||
// DeBruijnVertex v3 = new DeBruijnVertex("CT");
|
||||
// DeBruijnVertex v4 = new DeBruijnVertex("TG");
|
||||
// DeBruijnVertex v5 = new DeBruijnVertex("AG");
|
||||
// DeBruijnVertex v6 = new DeBruijnVertex("GG");
|
||||
// DeBruijnVertex v7 = new DeBruijnVertex("GA");
|
||||
// DeBruijnVertex v8 = new DeBruijnVertex("AA");
|
||||
//
|
||||
// graph.addVertices(v1, v2, v3, v4, v5, v6, v7, v8);
|
||||
// graph.addEdge(v1, v2, new DeBruijnEdge(false, 2));
|
||||
// graph.addEdge(v2, v3, new DeBruijnEdge(false, 3));
|
||||
// graph.addEdge(v2, v4, new DeBruijnEdge(false, 5));
|
||||
// graph.addEdge(v3, v5, new DeBruijnEdge(false, 3));
|
||||
// graph.addEdge(v4, v6, new DeBruijnEdge(false, 3));
|
||||
// graph.addEdge(v5, v7, new DeBruijnEdge(false, 2));
|
||||
// graph.addEdge(v6, v7, new DeBruijnEdge(false, 6));
|
||||
// graph.addEdge(v7, v8, new DeBruijnEdge(false, 2));
|
||||
//
|
||||
// graph.printGraph(new File("unittest.dot"), 1);
|
||||
//
|
||||
// DeBruijnAssemblyGraph expected = new DeBruijnAssemblyGraph();
|
||||
// DeBruijnVertex e1 = new DeBruijnVertex("ATC");
|
||||
// DeBruijnVertex e2 = new DeBruijnVertex("T");
|
||||
// DeBruijnVertex e3 = new DeBruijnVertex("G");
|
||||
// DeBruijnVertex e4 = new DeBruijnVertex("GAA");
|
||||
//
|
||||
// expected.addVertices(e1,e2,e3,e4);
|
||||
// expected.addEdge(e1, e2, new DeBruijnEdge(false, 3));
|
||||
// expected.addEdge(e1, e3, new DeBruijnEdge(false, 5));
|
||||
// expected.addEdge(e2, e4, new DeBruijnEdge(false, 2));
|
||||
// expected.addEdge(e3, e4, new DeBruijnEdge(false, 6));
|
||||
//
|
||||
// expected.printGraph(new File("expected.dot"), 1);
|
||||
//
|
||||
// tests.add(new Object[]{graph.clone(), expected});
|
||||
// }
|
||||
//
|
||||
// return tests.toArray(new Object[][]{});
|
||||
// }
|
||||
//
|
||||
// @Test(dataProvider = "SimpleMergeOperationsData", enabled = true)
|
||||
// public void testSimpleMergeOperations(final DeBruijnAssemblyGraph unmergedGraph, final DeBruijnAssemblyGraph expectedGraph) throws Exception {
|
||||
// final DeBruijnAssemblyGraph mergedGraph = (DeBruijnAssemblyGraph)unmergedGraph.clone();
|
||||
// DeBruijnAssembler.mergeNodes(mergedGraph);
|
||||
// mergedGraph.printGraph(new File("merged.dot"), 1);
|
||||
// DeBruijnAssembler.simplifyMergedGraph(mergedGraph);
|
||||
// mergedGraph.printGraph(new File("reduced.dot"), 1);
|
||||
// Assert.assertTrue(graphEquals(mergedGraph, expectedGraph));
|
||||
// }
|
||||
|
||||
@Test(enabled = !DEBUG)
|
||||
public void testPruneGraph() {
|
||||
DeBruijnAssemblyGraph graph = new DeBruijnAssemblyGraph();
|
||||
DeBruijnAssemblyGraph expectedGraph = new DeBruijnAssemblyGraph();
|
||||
|
|
@ -210,7 +268,7 @@ public class DeBruijnAssemblerUnitTest extends BaseTest {
|
|||
return true;
|
||||
}
|
||||
|
||||
@Test(enabled = true)
|
||||
@Test(enabled = !DEBUG)
|
||||
public void testReferenceCycleGraph() {
|
||||
String refCycle = "ATCGAGGAGAGCGCCCCGAGATATATATATATATATTTGCGAGCGCGAGCGTTTTAAAAATTTTAGACGGAGAGATATATATATATGGGAGAGGGGATATATATATATCCCCCC";
|
||||
String noCycle = "ATCGAGGAGAGCGCCCCGAGATATTATTTGCGAGCGCGAGCGTTTTAAAAATTTTAGACGGAGAGATGGGAGAGGGGATATATAATATCCCCCC";
|
||||
|
|
@ -221,7 +279,7 @@ public class DeBruijnAssemblerUnitTest extends BaseTest {
|
|||
Assert.assertTrue(g2 != null, "Reference non-cycle graph should not return null during creation.");
|
||||
}
|
||||
|
||||
@Test(enabled = true)
|
||||
@Test(enabled = !DEBUG)
|
||||
public void testLeftAlignCigarSequentially() {
|
||||
String preRefString = "GATCGATCGATC";
|
||||
String postRefString = "TTT";
|
||||
|
|
|
|||
|
|
@ -0,0 +1,78 @@
|
|||
/*
|
||||
* 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 org.broadinstitute.sting.BaseTest;
|
||||
import org.testng.Assert;
|
||||
import org.testng.annotations.Test;
|
||||
|
||||
public class KMerErrorCorrectorUnitTest extends BaseTest {
|
||||
@Test
|
||||
public void testMyData() {
|
||||
final KMerErrorCorrector corrector = new KMerErrorCorrector(3, 1, 2, 2);
|
||||
|
||||
corrector.addKmers(
|
||||
"ATG", "ATG", "ATG", "ATG",
|
||||
"ACC", "ACC", "ACC",
|
||||
"AAA", "AAA",
|
||||
"CTG", // -> ATG
|
||||
"NNA", // -> AAA
|
||||
"CCC", // => ACC
|
||||
"NNN", // => null
|
||||
"NNC" // => ACC [because of min count won't go to NNA]
|
||||
);
|
||||
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("ATG"), "ATG");
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("ACC"), "ACC");
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("AAA"), "AAA");
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("CTG"), "ATG");
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("NNA"), "AAA");
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("CCC"), "ACC");
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("NNN"), null);
|
||||
Assert.assertEquals(corrector.getErrorCorrectedKmer("NNC"), "ACC");
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue