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package org.broadinstitute.gatk.utils.variant;
import htsjdk.variant.variantcontext.*;
import htsjdk.variant.vcf.VCFConstants;
import org.broadinstitute.gatk.tools.walkers.genotyper.GenotypeLikelihoodCalculators;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.MathUtils;
import org.broadinstitute.gatk.utils.Utils;
import org.broadinstitute.gatk.utils.collections.Pair;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import java.util.*;
/**
* Variant context utilities related to merging variant-context instances.
*
* @author Valentin Ruano-Rubio <valentin@broadinstitute.org>
*/
public class ReferenceConfidenceVariantContextMerger {
private static Comparable combineAnnotationValues( final List<Comparable> array ) {
return MathUtils.median(array); // right now we take the median but other options could be explored
}
/**
* Merges VariantContexts from gVCFs into a single hybrid.
* Assumes that none of the input records are filtered.
*
* @param VCs collection of unsorted genomic VCs
* @param loc the current location
* @param refBase the reference allele to use if all contexts in the VC are spanning (i.e. don't start at the location in loc); if null, we'll return null in this case
* @param removeNonRefSymbolicAllele if true, remove the <NON_REF> allele from the merged VC
* @return new VariantContext representing the merge of all VCs or null if it not relevant
*/
public static VariantContext merge(final List<VariantContext> VCs, final GenomeLoc loc, final Byte refBase, final boolean removeNonRefSymbolicAllele) {
// this can happen if e.g. you are using a dbSNP file that spans a region with no gVCFs
if ( VCs == null || VCs.size() == 0 )
return null;
// establish the baseline info (sometimes from the first VC)
final VariantContext first = VCs.get(0);
final String name = first.getSource();
// ref allele
final Allele refAllele = determineReferenceAlleleGivenReferenceBase(VCs, loc, refBase);
if ( refAllele == null )
return null;
// FinalAlleleSet contains the alleles of the new resulting VC
// Using linked set in order to guarantee a stable order
final LinkedHashSet<Allele> finalAlleleSet = new LinkedHashSet<>(10);
// Reference goes first
finalAlleleSet.add(refAllele);
final Map<String, Object> attributes = new LinkedHashMap<>();
final Set<String> rsIDs = new LinkedHashSet<>(1); // most of the time there's one id
int depth = 0;
final Map<String, List<Comparable>> annotationMap = new LinkedHashMap<>();
final GenotypesContext genotypes = GenotypesContext.create();
final int variantContextCount = VCs.size();
// In this list we hold the mapping of each variant context alleles.
final List<Pair<VariantContext,List<Allele>>> vcAndNewAllelePairs = new ArrayList<>(variantContextCount);
// cycle through and add info from the other VCs
for ( final VariantContext vc : VCs ) {
// if this context doesn't start at the current location then it must be a spanning event (deletion or ref block)
final boolean isSpanningEvent = loc.getStart() != vc.getStart();
vcAndNewAllelePairs.add(new Pair<>(vc,isSpanningEvent ? replaceWithNoCalls(vc.getAlleles())
: remapAlleles(vc.getAlleles(), refAllele, finalAlleleSet)));
}
// Add <NON_REF> to the end if at all required in in the output.
if (!removeNonRefSymbolicAllele) finalAlleleSet.add(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
final List<Allele> allelesList = new ArrayList<>(finalAlleleSet);
for ( final Pair<VariantContext,List<Allele>> pair : vcAndNewAllelePairs ) {
final VariantContext vc = pair.getFirst();
final List<Allele> remappedAlleles = pair.getSecond();
mergeRefConfidenceGenotypes(genotypes, vc, remappedAlleles, allelesList);
// special case DP (add it up) for all events
if ( vc.hasAttribute(VCFConstants.DEPTH_KEY) ) {
depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
} else { // handle the gVCF case from the HaplotypeCaller
for( final Genotype gt : vc.getGenotypes() ) {
depth += (gt.hasExtendedAttribute("MIN_DP") ? Integer.parseInt((String)gt.getAnyAttribute("MIN_DP")) : (gt.hasDP() ? gt.getDP() : 0));
}
}
if ( loc.getStart() != vc.getStart() )
continue;
// special case ID (just preserve it)
if ( vc.hasID() ) rsIDs.add(vc.getID());
// add attributes
addReferenceConfidenceAttributes(vc.getAttributes(), annotationMap);
}
// when combining annotations use the median value from all input VCs which had annotations provided
for ( final Map.Entry<String, List<Comparable>> p : annotationMap.entrySet() ) {
if ( ! p.getValue().isEmpty() ) {
attributes.put(p.getKey(), combineAnnotationValues(p.getValue()));
}
}
if ( depth > 0 )
attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));
// remove stale AC and AF based attributes
removeStaleAttributesAfterMerge(attributes);
final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);
final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID).alleles(allelesList)
.chr(loc.getContig()).start(loc.getStart()).computeEndFromAlleles(allelesList, loc.getStart(), loc.getStart())
.genotypes(genotypes).unfiltered().attributes(new TreeMap<>(attributes)).log10PError(CommonInfo.NO_LOG10_PERROR); // we will need to re-genotype later
return builder.make();
}
/**
* Determines the ref allele given the provided reference base at this position
*
* @param VCs collection of unsorted genomic VCs
* @param loc the current location
* @param refBase the reference allele to use if all contexts in the VC are spanning
* @return new Allele or null if no reference allele/base is available
*/
private static Allele determineReferenceAlleleGivenReferenceBase(final List<VariantContext> VCs, final GenomeLoc loc, final Byte refBase) {
final Allele refAllele = GATKVariantContextUtils.determineReferenceAllele(VCs, loc);
if ( refAllele == null )
return ( refBase == null ? null : Allele.create(refBase, true) );
return refAllele;
}
/**
* Remove the stale attributes from the merged set
*
* @param attributes the attribute map
*/
private static void removeStaleAttributesAfterMerge(final Map<String, Object> attributes) {
attributes.remove(VCFConstants.ALLELE_COUNT_KEY);
attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
attributes.remove(VCFConstants.ALLELE_NUMBER_KEY);
attributes.remove(VCFConstants.MLE_ALLELE_COUNT_KEY);
attributes.remove(VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
attributes.remove(VCFConstants.END_KEY);
}
/**
* Adds attributes to the global map from the new context in a sophisticated manner
*
* @param myAttributes attributes to add from
* @param annotationMap map of annotations for combining later
*/
private static void addReferenceConfidenceAttributes(final Map<String, Object> myAttributes,
final Map<String, List<Comparable>> annotationMap) {
for ( final Map.Entry<String, Object> p : myAttributes.entrySet() ) {
final String key = p.getKey();
final Object value = p.getValue();
// add the annotation values to a list for combining later
List<Comparable> values = annotationMap.get(key);
if( values == null ) {
values = new ArrayList<>();
annotationMap.put(key, values);
}
try {
final String stringValue = value.toString();
// Branch to avoid unintentional, implicit type conversions that occur with the ? operator.
if (stringValue.contains("."))
values.add(Double.parseDouble(stringValue));
else
values.add(Integer.parseInt(stringValue));
} catch (final NumberFormatException e) {
// nothing to do
}
}
}
/**
* This method does a couple of things:
* <ul><li>
* remaps the vc alleles considering the differences between the final reference allele and its own reference,</li>
* <li>
* collects alternative alleles present in variant context and add them to the {@code finalAlleles} set.
* </li></ul>
*
* @param vcAlleles the variant context allele list.
* @param refAllele final reference allele.
* @param finalAlleles where to add the final set of non-ref called alleles.
* @return never {@code null}
*/
//TODO as part of a larger refactoring effort {@link #remapAlleles} can be merged with {@link GATKVariantContextUtils#remapAlleles}.
private static List<Allele> remapAlleles(final List<Allele> vcAlleles, final Allele refAllele, final LinkedHashSet<Allele> finalAlleles) {
final Allele vcRef = vcAlleles.get(0);
if (!vcRef.isReference()) throw new IllegalStateException("the first allele of the vc allele list must be reference");
final byte[] refBases = refAllele.getBases();
final int extraBaseCount = refBases.length - vcRef.getBases().length;
if (extraBaseCount < 0) throw new IllegalStateException("the wrong reference was selected");
final List<Allele> result = new ArrayList<>(vcAlleles.size());
for (final Allele a : vcAlleles) {
if (a.isReference()) {
result.add(refAllele);
} else if (a.isSymbolic()) {
result.add(a);
// we always skip <NON_REF> when adding to finalAlleles this is done outside if applies.
if (!a.equals(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE))
finalAlleles.add(a);
} else if (a.isCalled()) {
final Allele newAllele;
if (extraBaseCount > 0) {
final byte[] oldBases = a.getBases();
final byte[] newBases = Arrays.copyOf(oldBases,oldBases.length + extraBaseCount);
System.arraycopy(refBases,refBases.length - extraBaseCount,newBases,oldBases.length,extraBaseCount);
newAllele = Allele.create(newBases,false);
} else
newAllele = a;
result.add(newAllele);
finalAlleles.add(newAllele);
} else { // NO_CALL and strange miscellanea
result.add(a);
}
}
return result;
}
/**
* Replaces any alleles in the list with NO CALLS, except for the generic ALT allele
*
* @param alleles list of alleles to replace
* @return non-null list of alleles
*/
private static List<Allele> replaceWithNoCalls(final List<Allele> alleles) {
if ( alleles == null ) throw new IllegalArgumentException("list of alleles cannot be null");
final List<Allele> result = new ArrayList<>(alleles.size());
for ( final Allele allele : alleles )
result.add(allele.equals(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) ? allele : Allele.NO_CALL);
return result;
}
/**
* Merge into the context a new genotype represented by the given VariantContext for the provided list of target alleles.
* This method assumes that none of the alleles in the VC overlaps with any of the alleles in the set.
*
* @param mergedGenotypes the genotypes context to add to
* @param VC the Variant Context for the sample
* @param remappedAlleles the list of remapped alleles for the sample
* @param targetAlleles the list of target alleles
*/
private static void mergeRefConfidenceGenotypes(final GenotypesContext mergedGenotypes,
final VariantContext VC,
final List<Allele> remappedAlleles,
final List<Allele> targetAlleles) {
final int maximumPloidy = VC.getMaxPloidy(GATKVariantContextUtils.DEFAULT_PLOIDY);
// the map is different depending on the ploidy, so in order to keep this method flexible (mixed ploidies)
// we need to get a map done (lazily inside the loop) for each ploidy, up to the maximum possible.
final int[][] genotypeIndexMapsByPloidy = new int[maximumPloidy + 1][];
final int maximumAlleleCount = Math.max(remappedAlleles.size(),targetAlleles.size());
final int[] indexesOfRelevantAlleles = getIndexesOfRelevantAlleles(remappedAlleles, targetAlleles, VC.getStart());
for ( final Genotype g : VC.getGenotypes() ) {
final String name = g.getSampleName();
if ( mergedGenotypes.containsSample(name) )
continue;
final int ploidy = g.getPloidy();
final GenotypeBuilder genotypeBuilder = new GenotypeBuilder(g).alleles(GATKVariantContextUtils.noCallAlleles(g.getPloidy()));
if (g.hasPL()) {
// lazy initialization of the genotype index map by ploidy.
final int[] genotypeIndexMapByPloidy = genotypeIndexMapsByPloidy[ploidy] == null
? GenotypeLikelihoodCalculators.getInstance(ploidy, maximumAlleleCount).genotypeIndexMap(indexesOfRelevantAlleles)
: genotypeIndexMapsByPloidy[ploidy];
final int[] PLs = generatePL(g, genotypeIndexMapByPloidy);
final int[] AD = g.hasAD() ? generateAD(g.getAD(), indexesOfRelevantAlleles) : null;
genotypeBuilder.PL(PLs).AD(AD).noGQ();
}
mergedGenotypes.add(genotypeBuilder.make());
}
}
/**
* Composes a new likelihood array given the original genotype and the genotype index map.
*
* @param g the original genotype.
* @param genotypeIndexMapByPloidy genotype index map. The ith element indicates what genotype in {@code g} corresponds
* to the ith genotype in the return likelihoods array.
*
* @throws NullPointerException if {@code g} or {@code genotypeIndexMapByPloidy} is {@code null}, or if {@code g}
* does not contain likelihoods.
* @throws IndexOutOfBoundsException if {@code genotypeIndexMapByPloidy} contain non valid
* genotype indices given the likelihood array in {@code g}.
*
* @return never {@code null} but an array of exactly {@code genotypeIndexMapByPloidy.length} positions.
*/
private static int[] generatePL(final Genotype g, final int[] genotypeIndexMapByPloidy) {
final int[] PLs = new int[genotypeIndexMapByPloidy.length];
final int[] oldPLs = g.getPL();
for (int i = 0; i < PLs.length; i++)
PLs[i] = oldPLs[genotypeIndexMapByPloidy[i]];
return PLs;
}
/**
* Determines the allele mapping from myAlleles to the targetAlleles, substituting the generic "<ALT>" as appropriate.
* If the myAlleles set does not contain "<ALT>" as an allele, it throws an exception.
*
* @param remappedAlleles the list of alleles to evaluate
* @param targetAlleles the target list of alleles
* @param position position to use for error messages
* @return non-null array of ints representing indexes
*/
protected static int[] getIndexesOfRelevantAlleles(final List<Allele> remappedAlleles, final List<Allele> targetAlleles, final int position) {
if ( remappedAlleles == null || remappedAlleles.size() == 0 ) throw new IllegalArgumentException("The list of input alleles must not be null or empty");
if ( targetAlleles == null || targetAlleles.size() == 0 ) throw new IllegalArgumentException("The list of target alleles must not be null or empty");
if ( !remappedAlleles.contains(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE) )
throw new UserException("The list of input alleles must contain " + GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE + " as an allele but that is not the case at position " + position + "; please use the Haplotype Caller with gVCF output to generate appropriate records");
final int indexOfGenericAlt = remappedAlleles.indexOf(GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
final int[] indexMapping = new int[targetAlleles.size()];
// the reference alleles always match up (even if they don't appear to)
indexMapping[0] = 0;
// create the index mapping, using the <ALT> allele whenever such a mapping doesn't exist
for ( int i = 1; i < targetAlleles.size(); i++ ) {
final int indexOfRemappedAllele = remappedAlleles.indexOf(targetAlleles.get(i));
indexMapping[i] = indexOfRemappedAllele == -1 ? indexOfGenericAlt : indexOfRemappedAllele;
}
return indexMapping;
}
/**
* Generates a new AD array by adding zeros for missing alleles given the set of indexes of the Genotype's current
* alleles from the original AD.
*
* @param originalAD the original AD to extend
* @param indexesOfRelevantAlleles the indexes of the original alleles corresponding to the new alleles
* @return non-null array of new AD values
*/
protected static int[] generateAD(final int[] originalAD, final int[] indexesOfRelevantAlleles) {
if ( originalAD == null || indexesOfRelevantAlleles == null ) throw new IllegalArgumentException("The list of input AD values and alleles must not be null");
final int numADs = indexesOfRelevantAlleles.length;
final int[] newAD = new int[numADs];
for ( int i = 0; i < numADs; i++ ) {
final int oldIndex = indexesOfRelevantAlleles[i];
if ( oldIndex >= originalAD.length )
newAD[i] = 0;
else
newAD[i] = originalAD[oldIndex];
}
return newAD;
}
}