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package org.broadinstitute.gatk.tools.walkers.haplotypecaller;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import htsjdk.samtools.Cigar;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.*;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.activeregion.ActiveRegion;
import org.broadinstitute.gatk.utils.gga.GenotypingGivenAllelesUtils;
import org.broadinstitute.gatk.utils.haplotype.Haplotype;
import org.broadinstitute.gatk.utils.sam.CigarUtils;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import htsjdk.variant.variantcontext.VariantContext;
import java.io.File;
import java.io.PrintStream;
import java.util.*;
/**
* Abstract base class for all HaplotypeCaller assemblers
*
* User: ebanks
* Date: Mar 14, 2011
*/
public abstract class LocalAssemblyEngine {
private final static Logger logger = Logger.getLogger(LocalAssemblyEngine.class);
/**
* If false, we will only write out a region around the reference source
*/
private final static boolean PRINT_FULL_GRAPH_FOR_DEBUGGING = true;
public static final byte DEFAULT_MIN_BASE_QUALITY_TO_USE = (byte) 10;
private static final int MIN_HAPLOTYPE_REFERENCE_LENGTH = 30;
protected final int numBestHaplotypesPerGraph;
protected boolean debug = false;
protected boolean allowCyclesInKmerGraphToGeneratePaths = false;
protected boolean debugGraphTransformations = false;
protected boolean recoverDanglingBranches = true;
protected int minDanglingBranchLength = 0;
protected byte minBaseQualityToUseInAssembly = DEFAULT_MIN_BASE_QUALITY_TO_USE;
protected int pruneFactor = 2;
protected boolean errorCorrectKmers = false;
private PrintStream graphWriter = null;
/**
* Create a new LocalAssemblyEngine with all default parameters, ready for use
* @param numBestHaplotypesPerGraph the number of haplotypes to generate for each assembled graph
*/
protected LocalAssemblyEngine(final int numBestHaplotypesPerGraph) {
if ( numBestHaplotypesPerGraph < 1 ) throw new IllegalArgumentException("numBestHaplotypesPerGraph should be >= 1 but got " + numBestHaplotypesPerGraph);
this.numBestHaplotypesPerGraph = numBestHaplotypesPerGraph;
}
/**
* Main subclass function: given reads and a reference haplotype give us graphs to use for constructing
* non-reference haplotypes.
*
* @param reads the reads we're going to assemble
* @param refHaplotype the reference haplotype
* @return a non-null list of reads
*/
protected abstract List<AssemblyResult> assemble(List<GATKSAMRecord> reads, Haplotype refHaplotype, List<Haplotype> givenHaplotypes);
/**
* Main entry point into the assembly engine. Build a set of deBruijn graphs out of the provided reference sequence and list of reads
* @param activeRegion ActiveRegion object holding the reads which are to be used during assembly
* @param refHaplotype reference haplotype object
* @param fullReferenceWithPadding byte array holding the reference sequence with padding
* @param refLoc GenomeLoc object corresponding to the reference sequence with padding
* @param givenAlleles the alleles to inject into the haplotypes during GGA mode
* @param readErrorCorrector a ReadErrorCorrector object, if read are to be corrected before assembly. Can be null if no error corrector is to be used.
* @return the resulting assembly-result-set
*/
public AssemblyResultSet runLocalAssembly(final ActiveRegion activeRegion,
final Haplotype refHaplotype,
final byte[] fullReferenceWithPadding,
final GenomeLoc refLoc,
final List<VariantContext> givenAlleles,
final ReadErrorCorrector readErrorCorrector) {
if( activeRegion == null ) { throw new IllegalArgumentException("Assembly engine cannot be used with a null ActiveRegion."); }
if( activeRegion.getExtendedLoc() == null ) { throw new IllegalArgumentException("Active region must have an extended location."); }
if( refHaplotype == null ) { throw new IllegalArgumentException("Reference haplotype cannot be null."); }
if( fullReferenceWithPadding.length != refLoc.size() ) { throw new IllegalArgumentException("Reference bases and reference loc must be the same size."); }
if( pruneFactor < 0 ) { throw new IllegalArgumentException("Pruning factor cannot be negative"); }
// create the list of artificial haplotypes that should be added to the graph for GGA mode
final List<Haplotype> givenHaplotypes = GenotypingGivenAllelesUtils.composeGivenHaplotypes(refHaplotype, givenAlleles, activeRegion.getExtendedLoc());
// error-correct reads before clipping low-quality tails: some low quality bases might be good and we want to recover them
final List<GATKSAMRecord> correctedReads;
if (readErrorCorrector != null) {
// now correct all reads in active region after filtering/downsampling
// Note that original reads in active region are NOT modified by default, since they will be used later for GL computation,
// and we only want the read-error corrected reads for graph building.
readErrorCorrector.addReadsToKmers(activeRegion.getReads());
correctedReads = new ArrayList<>(readErrorCorrector.correctReads(activeRegion.getReads()));
} else {
correctedReads = activeRegion.getReads();
}
final List<SeqGraph> nonRefGraphs = new LinkedList<>();
final AssemblyResultSet resultSet = new AssemblyResultSet();
resultSet.setRegionForGenotyping(activeRegion);
resultSet.setFullReferenceWithPadding(fullReferenceWithPadding);
resultSet.setPaddedReferenceLoc(refLoc);
final GenomeLoc activeRegionExtendedLocation = activeRegion.getExtendedLoc();
refHaplotype.setGenomeLocation(activeRegionExtendedLocation);
resultSet.add(refHaplotype);
final Map<SeqGraph,AssemblyResult> assemblyResultByGraph = new HashMap<>();
// create the graphs by calling our subclass assemble method
for ( final AssemblyResult result : assemble(correctedReads, refHaplotype, givenHaplotypes) ) {
if ( result.getStatus() == AssemblyResult.Status.ASSEMBLED_SOME_VARIATION ) {
// do some QC on the graph
sanityCheckGraph(result.getGraph(), refHaplotype);
// add it to graphs with meaningful non-reference features
assemblyResultByGraph.put(result.getGraph(),result);
nonRefGraphs.add(result.getGraph());
}
}
findBestPaths (nonRefGraphs, refHaplotype, refLoc, activeRegionExtendedLocation, assemblyResultByGraph, resultSet);
// print the graphs if the appropriate debug option has been turned on
if ( graphWriter != null ) { printGraphs(nonRefGraphs); }
return resultSet;
}
@Ensures({"result.contains(refHaplotype)"})
protected List<Haplotype> findBestPaths(final List<SeqGraph> graphs, final Haplotype refHaplotype, final GenomeLoc refLoc, final GenomeLoc activeRegionWindow,
final Map<SeqGraph,AssemblyResult> assemblyResultByGraph, final AssemblyResultSet assemblyResultSet) {
// add the reference haplotype separately from all the others to ensure that it is present in the list of haplotypes
final Set<Haplotype> returnHaplotypes = new LinkedHashSet<>();
final int activeRegionStart = refHaplotype.getAlignmentStartHapwrtRef();
final ArrayList<KBestHaplotypeFinder> finders = new ArrayList<>(graphs.size());
int failedCigars = 0;
for( final SeqGraph graph : graphs ) {
final SeqVertex source = graph.getReferenceSourceVertex();
final SeqVertex sink = graph.getReferenceSinkVertex();
if ( source == null || sink == null ) throw new IllegalArgumentException("Both source and sink cannot be null but got " + source + " and sink " + sink + " for graph "+ graph);
final KBestHaplotypeFinder haplotypeFinder = new KBestHaplotypeFinder(graph,source,sink);
finders.add(haplotypeFinder);
final Iterator<KBestHaplotype> bestHaplotypes = haplotypeFinder.iterator(numBestHaplotypesPerGraph);
while (bestHaplotypes.hasNext()) {
final KBestHaplotype kBestHaplotype = bestHaplotypes.next();
final Haplotype h = kBestHaplotype.haplotype();
if( !returnHaplotypes.contains(h) ) {
final Cigar cigar = CigarUtils.calculateCigar(refHaplotype.getBases(),h.getBases());
if ( cigar == null ) {
failedCigars++; // couldn't produce a meaningful alignment of haplotype to reference, fail quietly
continue;
} else if( cigar.isEmpty() ) {
throw new IllegalStateException("Smith-Waterman alignment failure. Cigar = " + cigar + " with reference length " + cigar.getReferenceLength() +
" but expecting reference length of " + refHaplotype.getCigar().getReferenceLength());
} else if ( pathIsTooDivergentFromReference(cigar) || cigar.getReferenceLength() < MIN_HAPLOTYPE_REFERENCE_LENGTH ) {
// N cigar elements means that a bubble was too divergent from the reference so skip over this path
continue;
} else if( cigar.getReferenceLength() != refHaplotype.getCigar().getReferenceLength() ) { // SW failure
throw new IllegalStateException("Smith-Waterman alignment failure. Cigar = " + cigar + " with reference length "
+ cigar.getReferenceLength() + " but expecting reference length of " + refHaplotype.getCigar().getReferenceLength()
+ " ref = " + refHaplotype + " path " + new String(h.getBases()));
}
h.setCigar(cigar);
h.setAlignmentStartHapwrtRef(activeRegionStart);
h.setGenomeLocation(activeRegionWindow);
returnHaplotypes.add(h);
assemblyResultSet.add(h, assemblyResultByGraph.get(graph));
if ( debug )
logger.info("Adding haplotype " + h.getCigar() + " from graph with kmer " + graph.getKmerSize());
}
}
}
// Make sure that the ref haplotype is amongst the return haplotypes and calculate its score as
// the first returned by any finder.
if (!returnHaplotypes.contains(refHaplotype)) {
double refScore = Double.NaN;
for (final KBestHaplotypeFinder finder : finders) {
final double candidate = finder.score(refHaplotype);
if (Double.isNaN(candidate)) continue;
refScore = candidate;
break;
}
refHaplotype.setScore(refScore);
returnHaplotypes.add(refHaplotype);
}
if (failedCigars != 0)
logger.debug(String.format("failed to align some haplotypes (%d) back to the reference (loc=%s); these will be ignored.",failedCigars,refLoc.toString()));
if( debug ) {
if( returnHaplotypes.size() > 1 ) {
logger.info("Found " + returnHaplotypes.size() + " candidate haplotypes of " + returnHaplotypes.size() + " possible combinations to evaluate every read against.");
} else {
logger.info("Found only the reference haplotype in the assembly graph.");
}
for( final Haplotype h : returnHaplotypes ) {
logger.info( h.toString() );
logger.info( "> Cigar = " + h.getCigar() + " : " + h.getCigar().getReferenceLength() + " score " + h.getScore() + " ref " + h.isReference());
}
}
return new ArrayList<>(returnHaplotypes);
}
/**
* We use CigarOperator.N as the signal that an incomplete or too divergent bubble was found during bubble traversal
* @param c the cigar to test
* @return true if we should skip over this path
*/
@Requires("c != null")
private boolean pathIsTooDivergentFromReference( final Cigar c ) {
for( final CigarElement ce : c.getCigarElements() ) {
if( ce.getOperator().equals(CigarOperator.N) ) {
return true;
}
}
return false;
}
/**
* Print graph to file if debugGraphTransformations is enabled
* @param graph the graph to print
* @param file the destination file
*/
protected void printDebugGraphTransform(final BaseGraph graph, final File file) {
if ( debugGraphTransformations ) {
if ( PRINT_FULL_GRAPH_FOR_DEBUGGING )
graph.printGraph(file, pruneFactor);
else
graph.subsetToRefSource().printGraph(file, pruneFactor);
}
}
protected AssemblyResult cleanupSeqGraph(final SeqGraph seqGraph) {
printDebugGraphTransform(seqGraph, new File("sequenceGraph.1.dot"));
// the very first thing we need to do is zip up the graph, or pruneGraph will be too aggressive
seqGraph.zipLinearChains();
printDebugGraphTransform(seqGraph, new File("sequenceGraph.2.zipped.dot"));
// now go through and prune the graph, removing vertices no longer connected to the reference chain
seqGraph.removeSingletonOrphanVertices();
seqGraph.removeVerticesNotConnectedToRefRegardlessOfEdgeDirection();
printDebugGraphTransform(seqGraph, new File("sequenceGraph.3.pruned.dot"));
seqGraph.simplifyGraph();
printDebugGraphTransform(seqGraph, new File("sequenceGraph.4.merged.dot"));
// The graph has degenerated in some way, so the reference source and/or sink cannot be id'd. Can
// happen in cases where for example the reference somehow manages to acquire a cycle, or
// where the entire assembly collapses back into the reference sequence.
if ( seqGraph.getReferenceSourceVertex() == null || seqGraph.getReferenceSinkVertex() == null )
return new AssemblyResult(AssemblyResult.Status.JUST_ASSEMBLED_REFERENCE, seqGraph);
seqGraph.removePathsNotConnectedToRef();
seqGraph.simplifyGraph();
if ( seqGraph.vertexSet().size() == 1 ) {
// we've perfectly assembled into a single reference haplotype, add a empty seq vertex to stop
// the code from blowing up.
// TODO -- ref properties should really be on the vertices, not the graph itself
final SeqVertex complete = seqGraph.vertexSet().iterator().next();
final SeqVertex dummy = new SeqVertex("");
seqGraph.addVertex(dummy);
seqGraph.addEdge(complete, dummy, new BaseEdge(true, 0));
}
printDebugGraphTransform(seqGraph, new File("sequenceGraph.5.final.dot"));
return new AssemblyResult(AssemblyResult.Status.ASSEMBLED_SOME_VARIATION, seqGraph);
}
/**
* Perform general QC on the graph to make sure something hasn't gone wrong during assembly
* @param graph the graph to check
* @param refHaplotype the reference haplotype
*/
private <T extends BaseVertex, E extends BaseEdge> void sanityCheckGraph(final BaseGraph<T,E> graph, final Haplotype refHaplotype) {
sanityCheckReferenceGraph(graph, refHaplotype);
}
/**
* Make sure the reference sequence is properly represented in the provided graph
*
* @param graph the graph to check
* @param refHaplotype the reference haplotype
*/
private <T extends BaseVertex, E extends BaseEdge> void sanityCheckReferenceGraph(final BaseGraph<T,E> graph, final Haplotype refHaplotype) {
if( graph.getReferenceSourceVertex() == null ) {
throw new IllegalStateException("All reference graphs must have a reference source vertex.");
}
if( graph.getReferenceSinkVertex() == null ) {
throw new IllegalStateException("All reference graphs must have a reference sink vertex.");
}
if( !Arrays.equals(graph.getReferenceBytes(graph.getReferenceSourceVertex(), graph.getReferenceSinkVertex(), true, true), refHaplotype.getBases()) ) {
throw new IllegalStateException("Mismatch between the reference haplotype and the reference assembly graph path. for graph " + graph +
" graph = " + new String(graph.getReferenceBytes(graph.getReferenceSourceVertex(), graph.getReferenceSinkVertex(), true, true)) +
" haplotype = " + new String(refHaplotype.getBases())
);
}
}
/**
* Print the generated graphs to the graphWriter
* @param graphs a non-null list of graphs to print out
*/
private void printGraphs(final List<SeqGraph> graphs) {
final int writeFirstGraphWithSizeSmallerThan = 50;
graphWriter.println("digraph assemblyGraphs {");
for( final SeqGraph graph : graphs ) {
if ( debugGraphTransformations && graph.getKmerSize() >= writeFirstGraphWithSizeSmallerThan ) {
logger.info("Skipping writing of graph with kmersize " + graph.getKmerSize());
continue;
}
graph.printGraph(graphWriter, false, pruneFactor);
if ( debugGraphTransformations )
break;
}
graphWriter.println("}");
}
// -----------------------------------------------------------------------------------------------
//
// getter / setter routines for generic assembler properties
//
// -----------------------------------------------------------------------------------------------
public int getPruneFactor() {
return pruneFactor;
}
public void setPruneFactor(int pruneFactor) {
this.pruneFactor = pruneFactor;
}
public boolean shouldErrorCorrectKmers() {
return errorCorrectKmers;
}
public void setErrorCorrectKmers(boolean errorCorrectKmers) {
this.errorCorrectKmers = errorCorrectKmers;
}
public void setGraphWriter(PrintStream graphWriter) {
this.graphWriter = graphWriter;
}
public byte getMinBaseQualityToUseInAssembly() {
return minBaseQualityToUseInAssembly;
}
public void setMinBaseQualityToUseInAssembly(byte minBaseQualityToUseInAssembly) {
this.minBaseQualityToUseInAssembly = minBaseQualityToUseInAssembly;
}
public boolean isDebug() {
return debug;
}
public void setDebug(boolean debug) {
this.debug = debug;
}
public boolean isAllowCyclesInKmerGraphToGeneratePaths() {
return allowCyclesInKmerGraphToGeneratePaths;
}
public void setAllowCyclesInKmerGraphToGeneratePaths(boolean allowCyclesInKmerGraphToGeneratePaths) {
this.allowCyclesInKmerGraphToGeneratePaths = allowCyclesInKmerGraphToGeneratePaths;
}
public boolean isDebugGraphTransformations() {
return debugGraphTransformations;
}
public void setDebugGraphTransformations(boolean debugGraphTransformations) {
this.debugGraphTransformations = debugGraphTransformations;
}
public boolean isRecoverDanglingBranches() { return recoverDanglingBranches; }
public void setRecoverDanglingBranches(final boolean recoverDanglingBranches) {
this.recoverDanglingBranches = recoverDanglingBranches;
}
public void setMinDanglingBranchLength(final int minDanglingBranchLength) { this.minDanglingBranchLength = minDanglingBranchLength; }
}