Merge pull request #938 from broadinstitute/eb_fix_spanning_deletions_in_genotyping
Added a fix for genotyping positions over spanning deletions.
This commit is contained in:
Eric Banks
commit
53a34cea4a
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@ -88,9 +88,6 @@ import java.util.*;
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*/
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public class ReferenceConfidenceModel {
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//public final static String INDEL_INFORMATIVE_DEPTH = "CD"; // temporarily taking this extra genotype level information out for now
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public final static String ALTERNATE_ALLELE_STRING = "ALT"; // arbitrary alternate allele
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private final GenomeLocParser genomeLocParser;
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private final SampleList samples;
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@ -138,9 +135,7 @@ public class ReferenceConfidenceModel {
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*/
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public Set<VCFHeaderLine> getVCFHeaderLines() {
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final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>();
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// TODO - do we need a new kind of VCF Header subclass for specifying arbitrary alternate alleles?
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headerLines.add(new VCFSimpleHeaderLine(ALTERNATE_ALLELE_STRING, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE_NAME, "Represents any possible alternative allele at this location"));
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//headerLines.add(new VCFFormatHeaderLine(INDEL_INFORMATIVE_DEPTH, 1, VCFHeaderLineType.Integer, "Number of reads at locus that are informative about an indel of size <= " + indelInformativeDepthIndelSize));
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headerLines.add(new VCFSimpleHeaderLine(GATKVCFConstants.SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE_NAME, "Represents any possible alternative allele at this location"));
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return headerLines;
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}
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@ -165,6 +165,8 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
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// take care of the VCF headers
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final Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit());
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final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);
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headerLines.add(new VCFSimpleHeaderLine(GATKVCFConstants.SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG, GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_NAME, "Represents any possible spanning deletion allele at this location"));
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headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); // needed for gVCFs without DP tags
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final Set<String> samples = SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
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final VCFHeader vcfHeader = new VCFHeader(headerLines, samples);
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@ -217,10 +217,13 @@ public class GenotypeGVCFs extends RodWalker<VariantContext, VariantContextWrite
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final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);
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headerLines.addAll(annotationEngine.getVCFAnnotationDescriptions());
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headerLines.addAll(genotypingEngine.getAppropriateVCFInfoHeaders());
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// add the pool values for each genotype
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// add headers for annotations added by this tool
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headerLines.add(new VCFSimpleHeaderLine(GATKVCFConstants.SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG, GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE_NAME, "Represents any possible spanning deletion allele at this location"));
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_COUNT_KEY));
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headerLines.add(GATKVCFHeaderLines.getInfoLine(GATKVCFConstants.MLE_ALLELE_FREQUENCY_KEY));
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headerLines.add(GATKVCFHeaderLines.getFormatLine(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY));
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headerLines.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.DEPTH_KEY)); // needed for gVCFs without DP tags
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if ( dbsnp != null && dbsnp.dbsnp.isBound() )
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VCFStandardHeaderLines.addStandardInfoLines(headerLines, true, VCFConstants.DBSNP_KEY);
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@ -113,20 +113,27 @@ public class ReferenceConfidenceVariantContextMerger {
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final Map<String, List<Comparable>> annotationMap = new LinkedHashMap<>();
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final GenotypesContext genotypes = GenotypesContext.create();
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final int variantContextCount = VCs.size();
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// In this list we hold the mapping of each variant context alleles.
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final List<Pair<VariantContext,List<Allele>>> vcAndNewAllelePairs = new ArrayList<>(variantContextCount);
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final List<Pair<VariantContext,List<Allele>>> vcAndNewAllelePairs = new ArrayList<>(VCs.size());
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// Keep track of whether we saw a spanning deletion and a non-spanning event
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boolean sawSpanningDeletion = false;
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boolean sawNonSpanningEvent = false;
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// cycle through and add info from the other VCs
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for ( final VariantContext vc : VCs ) {
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// if this context doesn't start at the current location then it must be a spanning event (deletion or ref block)
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final boolean isSpanningEvent = loc.getStart() != vc.getStart();
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// record whether it's also a spanning deletion/event (we know this because the VariantContext type is no
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// longer "symbolic" but "mixed" because there are real alleles mixed in with the symbolic non-ref allele)
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sawSpanningDeletion |= ( isSpanningEvent && vc.isMixed() ) || vc.getAlternateAlleles().contains(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE);
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sawNonSpanningEvent |= ( !isSpanningEvent && vc.isMixed() );
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vcAndNewAllelePairs.add(new Pair<>(vc,isSpanningEvent ? replaceWithNoCalls(vc.getAlleles())
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: remapAlleles(vc.getAlleles(), refAllele, finalAlleleSet)));
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vcAndNewAllelePairs.add(new Pair<>(vc, isSpanningEvent ? replaceWithNoCallsAndDels(vc) : remapAlleles(vc, refAllele, finalAlleleSet)));
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}
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// Add <NON_REF> to the end if at all required in in the output.
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// Add <DEL> and <NON_REF> to the end if at all required in in the output.
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if ( sawSpanningDeletion && (sawNonSpanningEvent || !removeNonRefSymbolicAllele) ) finalAlleleSet.add(GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE);
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if (!removeNonRefSymbolicAllele) finalAlleleSet.add(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
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final List<Allele> allelesList = new ArrayList<>(finalAlleleSet);
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@ -171,13 +178,27 @@ public class ReferenceConfidenceVariantContextMerger {
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final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);
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// note that in order to calculate the end position, we need a list of alleles that doesn't include anything symbolic
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final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID).alleles(allelesList)
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.chr(loc.getContig()).start(loc.getStart()).computeEndFromAlleles(allelesList, loc.getStart(), loc.getStart())
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.chr(loc.getContig()).start(loc.getStart()).computeEndFromAlleles(nonSymbolicAlleles(allelesList), loc.getStart(), loc.getStart())
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.genotypes(genotypes).unfiltered().attributes(new TreeMap<>(attributes)).log10PError(CommonInfo.NO_LOG10_PERROR); // we will need to re-genotype later
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return builder.make();
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}
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/**
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* @param list the original alleles list
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* @return a non-null list of non-symbolic alleles
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*/
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private static List<Allele> nonSymbolicAlleles(final List<Allele> list) {
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final List<Allele> result = new ArrayList<>(list.size());
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for ( final Allele allele : list ) {
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if ( !allele.isSymbolic() )
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result.add(allele);
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}
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return result;
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}
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/**
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* Determines the ref allele given the provided reference base at this position
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*
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@ -246,27 +267,28 @@ public class ReferenceConfidenceVariantContextMerger {
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* collects alternative alleles present in variant context and add them to the {@code finalAlleles} set.
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* </li></ul>
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*
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* @param vcAlleles the variant context allele list.
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* @param refAllele final reference allele.
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* @param vc the variant context.
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* @param refAllele final reference allele.
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* @param finalAlleles where to add the final set of non-ref called alleles.
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* @return never {@code null}
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*/
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//TODO as part of a larger refactoring effort {@link #remapAlleles} can be merged with {@link GATKVariantContextUtils#remapAlleles}.
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private static List<Allele> remapAlleles(final List<Allele> vcAlleles, final Allele refAllele, final LinkedHashSet<Allele> finalAlleles) {
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final Allele vcRef = vcAlleles.get(0);
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if (!vcRef.isReference()) throw new IllegalStateException("the first allele of the vc allele list must be reference");
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private static List<Allele> remapAlleles(final VariantContext vc, final Allele refAllele, final LinkedHashSet<Allele> finalAlleles) {
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final Allele vcRef = vc.getReference();
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final byte[] refBases = refAllele.getBases();
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final int extraBaseCount = refBases.length - vcRef.getBases().length;
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if (extraBaseCount < 0) throw new IllegalStateException("the wrong reference was selected");
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final List<Allele> result = new ArrayList<>(vcAlleles.size());
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for (final Allele a : vcAlleles) {
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if (a.isReference()) {
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result.add(refAllele);
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} else if (a.isSymbolic()) {
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final List<Allele> result = new ArrayList<>(vc.getNAlleles());
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result.add(refAllele);
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for (final Allele a : vc.getAlternateAlleles()) {
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if (a.isSymbolic()) {
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result.add(a);
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// we always skip <NON_REF> when adding to finalAlleles this is done outside if applies.
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if (!a.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE))
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// we always skip <NON_REF> when adding to finalAlleles; this is done outside if applies.
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// we also skip <*DEL> if there isn't a real alternate allele.
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if ( !a.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE) && !vc.isSymbolic() )
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finalAlleles.add(a);
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} else if (a.isCalled()) {
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final Allele newAllele;
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@ -287,17 +309,31 @@ public class ReferenceConfidenceVariantContextMerger {
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}
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/**
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* Replaces any alleles in the list with NO CALLS, except for the generic ALT allele
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* Replaces any alleles in the VariantContext with NO CALLS or the symbolic deletion allele as appropriate, except for the generic ALT allele
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*
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* @param alleles list of alleles to replace
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* @param vc VariantContext with the alleles to replace
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* @return non-null list of alleles
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*/
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private static List<Allele> replaceWithNoCalls(final List<Allele> alleles) {
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if ( alleles == null ) throw new IllegalArgumentException("list of alleles cannot be null");
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private static List<Allele> replaceWithNoCallsAndDels(final VariantContext vc) {
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if ( vc == null ) throw new IllegalArgumentException("VariantContext cannot be null");
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final List<Allele> result = new ArrayList<>(alleles.size());
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for ( final Allele allele : alleles )
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result.add(allele.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE) ? allele : Allele.NO_CALL);
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final List<Allele> result = new ArrayList<>(vc.getNAlleles());
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// no-call the reference allele
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result.add(Allele.NO_CALL);
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// handle the alternate alleles
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for ( final Allele allele : vc.getAlternateAlleles() ) {
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final Allele replacement;
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if ( allele.equals(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE) )
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replacement = allele;
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else if ( allele.length() < vc.getReference().length() )
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replacement = GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE;
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else
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replacement = Allele.NO_CALL;
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result.add(replacement);
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}
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return result;
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}
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@ -387,43 +423,16 @@ public class ReferenceConfidenceVariantContextMerger {
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throw new UserException("The list of input alleles must contain " + GATKVCFConstants.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");
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final int indexOfNonRef = remappedAlleles.indexOf(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
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//if the refs don't match then let the non-ref allele be the most likely of the alts
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//TODO: eventually it would be nice to be able to trim alleles for spanning events to see if they really do have the same ref
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final boolean refsMatch = targetAlleles.get(0).equals(remappedAlleles.get(0),false);
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final int indexOfBestAlt;
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if (!refsMatch && g.hasPL()) {
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final int[] PLs = g.getPL().clone();
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PLs[0] = Integer.MAX_VALUE; //don't pick 0/0
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final int indexOfBestAltPL = MathUtils.minElementIndex(PLs);
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GenotypeLikelihoods.GenotypeLikelihoodsAllelePair pair = GenotypeLikelihoods.getAllelePair(indexOfBestAltPL);
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indexOfBestAlt = pair.alleleIndex2;
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}
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else
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indexOfBestAlt = indexOfNonRef;
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final int[] indexMapping = new int[targetAlleles.size()];
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// the reference likelihoods should always map to each other (even if the alleles don't)
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indexMapping[0] = 0;
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// create the index mapping, using the <ALT> allele whenever such a mapping doesn't exist
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final int targetNonRef = targetAlleles.indexOf(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
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final boolean targetHasNonRef = targetNonRef != -1;
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final int lastConcreteAlt = targetHasNonRef ? targetAlleles.size()-2 : targetAlleles.size()-1;
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for ( int i = 1; i <= lastConcreteAlt; i++ ) {
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// create the index mapping, using the <NON-REF> allele whenever such a mapping doesn't exist
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for ( int i = 1; i < targetAlleles.size(); i++ ) {
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final int indexOfRemappedAllele = remappedAlleles.indexOf(targetAlleles.get(i));
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indexMapping[i] = indexOfRemappedAllele == -1 ? indexOfNonRef : indexOfRemappedAllele;
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}
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if (targetHasNonRef) {
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if (refsMatch) {
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final int indexOfRemappedAllele = remappedAlleles.indexOf(targetAlleles.get(targetNonRef));
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indexMapping[targetNonRef] = indexOfRemappedAllele == -1 ? indexOfNonRef : indexOfRemappedAllele;
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}
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else {
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indexMapping[targetNonRef] = indexOfBestAlt;
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}
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}
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return indexMapping;
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}
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@ -100,7 +100,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
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" -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
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" -L " + privateTestDir + "tetraploid-gvcfs.intervals",
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1,
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Arrays.asList("7b3153135e4f8e1d137d3f4beb46f182"));
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Arrays.asList("ebe26077809961f53d5244643d24fd45"));
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executeTest("combineSingleSamplePipelineGVCF", spec);
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}
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@ -112,7 +112,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
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" -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
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" -L " + privateTestDir + "tetraploid-gvcfs.intervals",
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1,
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Arrays.asList("4f546634213ece6f08ec9258620b92bb"));
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Arrays.asList("2d36a5f996cad47e5d05fcd78f6e572e"));
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executeTest("combineSingleSamplePipelineGVCF", spec);
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}
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@ -190,7 +190,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
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@Test
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public void testMD5s() throws Exception {
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final String cmd = baseTestString(" -L 1:69485-69791");
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("b7c753452ab0c05f9cee538e420b87fa"));
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("83ea9f4a9aadb1218c21c9d3780e8009"));
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spec.disableShadowBCF();
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executeTest("testMD5s", spec);
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}
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@ -198,7 +198,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
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@Test
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public void testBasepairResolutionOutput() throws Exception {
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final String cmd = baseTestString(" -L 1:69485-69791 --convertToBasePairResolution");
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("bb6420ead95da4c72e76ca4bf5860ef0"));
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("f153cb6e986efc9b50f0b8833fe5d3da"));
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spec.disableShadowBCF();
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executeTest("testBasepairResolutionOutput", spec);
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}
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@ -206,16 +206,27 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
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@Test
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public void testBreakBlocks() throws Exception {
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final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5");
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("dd31182124c4b78a8a03edb1e0cf618b"));
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("6626ff272e7e76fba091f5bde4a1f963"));
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spec.disableShadowBCF();
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executeTest("testBreakBlocks", spec);
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}
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@Test
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public void testSpanningDeletions() {
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WalkerTestSpec spec = new WalkerTestSpec(
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"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
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" -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf",
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1,
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Arrays.asList("fba48ce2bf8761366ff2cd0b45d0421f"));
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spec.disableShadowBCF();
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executeTest("testSpanningDeletions", spec);
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}
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@Test
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public void testWrongReferenceBaseBugFix() throws Exception {
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final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf"
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+ " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header");
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("75d81c247bef5e394b4a2d4126aee2b3"));
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("331c1a4a6a72ea1617c1697a5d945d56"));
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spec.disableShadowBCF();
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executeTest("testWrongReferenceBaseBugFix",spec);
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@ -224,7 +235,7 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
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@Test
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public void testBasepairResolutionInput() throws Exception {
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final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf";
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("994ff5c219c683635eadc1624cbbda74"));
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final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("207e89b5677fbf0ef4d1ff768262cf0c"));
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spec.disableShadowBCF();
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executeTest("testBasepairResolutionInput", spec);
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}
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@ -82,7 +82,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf", b37KGReference),
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1,
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Arrays.asList("23ff3e22262929138ca1f00fc111cadf"));
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Arrays.asList("4dfea9a9b1a77c4c6b9edc61f9ea8da2"));
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executeTest("testUpdatePGT", spec);
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}
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@ -91,7 +91,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
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|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString(" -V " + privateTestDir + "testUpdatePGT.vcf -A StrandAlleleCountsBySample", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("88fa4a021e4aac9a0e48bd54b2949ece"));
|
||||
Arrays.asList("a96b79e7c3689c8d5506083cb6d27390"));
|
||||
executeTest("testUpdatePGT, adding StrandAlleleCountsBySample annotation", spec);
|
||||
}
|
||||
|
||||
|
|
@ -103,7 +103,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-20,000,000", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("06b4e2589c5b903f7c51ae9968bebe77"));
|
||||
Arrays.asList("bf3c1982ab6ffee410cb6a1fff6e7105"));
|
||||
executeTest("combineSingleSamplePipelineGVCF", spec);
|
||||
}
|
||||
|
||||
|
|
@ -115,7 +115,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "tetraploid-gvcf-3.vcf" +
|
||||
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("599394c205c1d6641b9bebabbd29e13c"));
|
||||
Arrays.asList("47d454936dc1f17cf4c4f84f02841346"));
|
||||
executeTest("combineSingleSamplePipelineGVCF", spec);
|
||||
}
|
||||
|
||||
|
|
@ -127,7 +127,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "diploid-gvcf-3.vcf" +
|
||||
" -L " + privateTestDir + "tetraploid-gvcfs.intervals", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("f7d5344a85e6d7fc2437d4253b424cb0"));
|
||||
Arrays.asList("5d79ea9de8ada8520d01284cf0c9f720"));
|
||||
executeTest("combineSingleSamplePipelineGVCF", spec);
|
||||
}
|
||||
|
||||
|
|
@ -139,7 +139,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" --includeNonVariantSites -L 20:10,030,000-10,033,000 -L 20:10,386,000-10,386,500", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("c9e4d1e52ee1f3a5233f1fb100f24d5e"));
|
||||
Arrays.asList("d69b43cac448f45218e77308fc01e9e6"));
|
||||
executeTest("combineSingleSamplePipelineGVCF_includeNonVariants", spec);
|
||||
}
|
||||
|
||||
|
|
@ -152,7 +152,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-20,000,000", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("aa19980b9a525afed43e98c821114ae5"));
|
||||
Arrays.asList("7c93d82758bfb6e7efec257ef8a46217"));
|
||||
executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
|
||||
}
|
||||
|
||||
|
|
@ -164,7 +164,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
|
||||
" -L 20:10,000,000-11,000,000 --dbsnp " + b37dbSNP132, b37KGReference),
|
||||
1,
|
||||
Arrays.asList("f23c9d62542a69b5cbf0e9f89fdd235d"));
|
||||
Arrays.asList("5b60a7a9575ea83407aa61123960a0cc"));
|
||||
executeTest("combineSingleSamplePipelineGVCF_addDbsnp", spec);
|
||||
}
|
||||
|
||||
|
|
@ -174,7 +174,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:69485-69791 -o %s -R " + b37KGReference +
|
||||
" -V " + privateTestDir + "gvcfExample1.vcf",
|
||||
1,
|
||||
Arrays.asList("d602d9e5d336798e4ccb52d2b5f91677"));
|
||||
Arrays.asList("9e59b94c84dd673b8db9d35cae7e0f68"));
|
||||
executeTest("testJustOneSample", spec);
|
||||
}
|
||||
|
||||
|
|
@ -185,14 +185,14 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V " + privateTestDir + "gvcfExample1.vcf" +
|
||||
" -V " + privateTestDir + "gvcfExample2.vcf",
|
||||
1,
|
||||
Arrays.asList("6c6d6ef90386eb6c6ed649379aac0c13"));
|
||||
Arrays.asList("8407cb9a1ab34e705e5a54a0d4146d84"));
|
||||
executeTest("testSamplesWithDifferentLs", spec);
|
||||
}
|
||||
|
||||
@Test(enabled = true)
|
||||
public void testNoPLsException() {
|
||||
// Test with input files with (1) 0/0 and (2) ./.
|
||||
final String md5 = "d04b32cf2fa97d303ff7fdc779a653d4";
|
||||
final String md5 = "3e69805dc1c0ada0a050a65b89ecab30";
|
||||
WalkerTestSpec spec1 = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -L 1:1115550-1115551 -o %s -R " + hg19Reference +
|
||||
" --variant " + privateTestDir + "combined_genotype_gvcf_exception.vcf",
|
||||
|
|
@ -212,7 +212,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseBPResolutionString("-nda"),
|
||||
1,
|
||||
Arrays.asList("7132a43d93a9855d03b27b4b0381194c"));
|
||||
Arrays.asList("5a036de16b7a87626d2b76727376d9df"));
|
||||
executeTest("testNDA", spec);
|
||||
}
|
||||
|
||||
|
|
@ -221,7 +221,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseBPResolutionString("-maxAltAlleles 1"),
|
||||
1,
|
||||
Arrays.asList("07844593a4e1ff1110ef8c1de42cc290"));
|
||||
Arrays.asList("2f3e6879fa27128a8be7b067ded78966"));
|
||||
executeTest("testMaxAltAlleles", spec);
|
||||
}
|
||||
|
||||
|
|
@ -230,7 +230,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseBPResolutionString("-stand_call_conf 300 -stand_emit_conf 100"),
|
||||
1,
|
||||
Arrays.asList("56caad762b26479ba5e2cc99222b9030"));
|
||||
Arrays.asList("2e4a1ad71e8fc127b594077166c0344b"));
|
||||
executeTest("testStandardConf", spec);
|
||||
}
|
||||
|
||||
|
|
@ -274,7 +274,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
" -V:combined2 " + privateTestDir + "combine.single.sample.pipeline.combined.vcf" +
|
||||
" --uniquifySamples", b37KGReference),
|
||||
1,
|
||||
Arrays.asList("ba36b36145e038e3cb004adf11bce96c"));
|
||||
Arrays.asList("9a472c4e101fff4892efb9255c5cd8b3"));
|
||||
executeTest("testUniquifiedSamples", spec);
|
||||
|
||||
}
|
||||
|
|
@ -311,4 +311,173 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
|
|||
return attributeValues;
|
||||
}
|
||||
|
||||
/**
|
||||
* Section to test spanning deletions
|
||||
*/
|
||||
@Test
|
||||
public void testSpanningDeletions() throws IOException {
|
||||
final String gvcf1 = privateTestDir + "spanningDel.1.g.vcf";
|
||||
final String gvcf2 = privateTestDir + "spanningDel.2.g.vcf";
|
||||
final String gvcf3 = privateTestDir + "spanningDel.3.g.vcf";
|
||||
|
||||
// create the genotyped VCF to use as a basis for comparison against all of the combined versions
|
||||
// case 0: GenotypeGVCFs(1.g.vcf, 2.g.vcf, 3.g.vcf)
|
||||
final WalkerTestSpec genotypeBase = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3,
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
genotypeBase.disableShadowBCF();
|
||||
final File genotypeBaseVCF = executeTest("genotypeBase", genotypeBase).getFirst().get(0);
|
||||
final List<VariantContext> BASE_VARIANT_CONTEXTS = getVariantContexts(genotypeBaseVCF);
|
||||
|
||||
// case 1: GenotypeGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf), 3.g.vcf)
|
||||
final WalkerTestSpec combine12 = new WalkerTestSpec(
|
||||
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + gvcf1 + " -V " + gvcf2,
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
combine12.disableShadowBCF();
|
||||
final File combined_gVCF12 = executeTest("combine12", combine12).getFirst().get(0);
|
||||
final WalkerTestSpec genotype12_3 = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + combined_gVCF12.getAbsolutePath() + " -V " + gvcf3,
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
genotype12_3.disableShadowBCF();
|
||||
final File genotype12_3VCF = executeTest("genotype12_3", genotype12_3).getFirst().get(0);
|
||||
final List<VariantContext> VARIANT_CONTEXTS_12_3 = getVariantContexts(genotype12_3VCF);
|
||||
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_12_3);
|
||||
|
||||
// case 2: GenotypeGVCFs(CombineGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf), 3.g.vcf))
|
||||
final WalkerTestSpec combine12then3 = new WalkerTestSpec(
|
||||
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + combined_gVCF12 + " -V " + gvcf3,
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
combine12then3.disableShadowBCF();
|
||||
final File combined_gVCF12then3 = executeTest("combined_gVCF12then3", combine12then3).getFirst().get(0);
|
||||
final WalkerTestSpec genotype12then3 = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + combined_gVCF12then3.getAbsolutePath(),
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
genotype12then3.disableShadowBCF();
|
||||
final File genotype12then3VCF = executeTest("genotype12then3", genotype12then3).getFirst().get(0);
|
||||
final List<VariantContext> VARIANT_CONTEXTS_12then3 = getVariantContexts(genotype12then3VCF);
|
||||
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_12then3);
|
||||
|
||||
// case 3: GenotypeGVCFs(CombineGVCFs(CombineGVCFs(1.g.vcf, 3.g.vcf), 2.g.vcf))
|
||||
final WalkerTestSpec combine13 = new WalkerTestSpec(
|
||||
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + gvcf1 + " -V " + gvcf3,
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
combine13.disableShadowBCF();
|
||||
final File combined_gVCF13 = executeTest("combine13", combine13).getFirst().get(0);
|
||||
final WalkerTestSpec combine13then2 = new WalkerTestSpec(
|
||||
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + combined_gVCF13 + " -V " + gvcf2,
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
combine13then2.disableShadowBCF();
|
||||
final File combined_gVCF13then2 = executeTest("combined_gVCF13then2", combine13then2).getFirst().get(0);
|
||||
final WalkerTestSpec genotype13then2 = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + combined_gVCF13then2.getAbsolutePath(),
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
genotype13then2.disableShadowBCF();
|
||||
final File genotype13then2VCF = executeTest("genotype13then2", genotype13then2).getFirst().get(0);
|
||||
final List<VariantContext> VARIANT_CONTEXTS_13then2 = getVariantContexts(genotype13then2VCF);
|
||||
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_13then2);
|
||||
|
||||
// case 4: GenotypeGVCFs(CombineGVCFs(1.g.vcf, 2.g.vcf, 3.g.vcf))
|
||||
final WalkerTestSpec combine123 = new WalkerTestSpec(
|
||||
"-T CombineGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + gvcf1 + " -V " + gvcf2 + " -V " + gvcf3,
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
combine123.disableShadowBCF();
|
||||
final File combined_gVCF123 = executeTest("combine123", combine123).getFirst().get(0);
|
||||
final WalkerTestSpec genotype123 = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + combined_gVCF123.getAbsolutePath(),
|
||||
1,
|
||||
Arrays.asList(""));
|
||||
genotype123.disableShadowBCF();
|
||||
final File genotype123VCF = executeTest("genotype123", genotype123).getFirst().get(0);
|
||||
final List<VariantContext> VARIANT_CONTEXTS_123 = getVariantContexts(genotype123VCF);
|
||||
testVCsAreEqual(BASE_VARIANT_CONTEXTS, VARIANT_CONTEXTS_123);
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns a list of VariantContext records from a VCF file
|
||||
*
|
||||
* @param vcfFile VCF file
|
||||
*
|
||||
* @throws IOException if the file does not exist or can not be opened
|
||||
*
|
||||
* @return list of VariantContext records
|
||||
*/
|
||||
private static List<VariantContext> getVariantContexts(final File vcfFile) throws IOException {
|
||||
final VCFCodec codec = new VCFCodec();
|
||||
final FileInputStream s = new FileInputStream(vcfFile);
|
||||
final LineIterator lineIteratorVCF = codec.makeSourceFromStream(new PositionalBufferedStream(s));
|
||||
codec.readHeader(lineIteratorVCF);
|
||||
|
||||
final List<VariantContext> VCs = new ArrayList<>();
|
||||
while ( lineIteratorVCF.hasNext() ) {
|
||||
final String line = lineIteratorVCF.next();
|
||||
Assert.assertFalse(line == null);
|
||||
VCs.add(codec.decode(line));
|
||||
}
|
||||
|
||||
return VCs;
|
||||
}
|
||||
|
||||
private static void testVCsAreEqual(final List<VariantContext> VCs1, final List<VariantContext> VCs2) {
|
||||
Assert.assertEquals(VCs1.size(), VCs2.size(), "number of Variant Contexts");
|
||||
for ( int i = 0; i < VCs1.size(); i++ ) {
|
||||
final VariantContext vc1 = VCs1.get(i);
|
||||
final VariantContext vc2 = VCs2.get(i);
|
||||
Assert.assertEquals(vc1.toStringDecodeGenotypes(), vc2.toStringDecodeGenotypes());
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private static final String simpleSpanningDeletionsMD5 = "e8616a396d40b4918ad30189856ceb01";
|
||||
|
||||
@Test(enabled = true)
|
||||
public void testSpanningDeletionsMD5() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf",
|
||||
1,
|
||||
Arrays.asList(simpleSpanningDeletionsMD5));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testSpanningDeletionsMD5", spec);
|
||||
}
|
||||
|
||||
@Test(enabled = true)
|
||||
public void testSpanningDeletionsFromCombinedGVCF() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + privateTestDir + "spanningDel.combined.g.vcf",
|
||||
1,
|
||||
Arrays.asList(simpleSpanningDeletionsMD5));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testSpanningDeletionsFromCombinedGVCFMD5", spec);
|
||||
}
|
||||
|
||||
@Test(enabled = true)
|
||||
public void testMultipleSpanningDeletionsMD5() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
"-T GenotypeGVCFs --no_cmdline_in_header -o %s -R " + b37KGReference +
|
||||
" -V " + privateTestDir + "spanningDel.1.g.vcf -V " + privateTestDir + "spanningDel.2.g.vcf -V " + privateTestDir + "spanningDel.3.g.vcf",
|
||||
1,
|
||||
Arrays.asList("1c418229117bc8f148a69eda9c496309"));
|
||||
spec.disableShadowBCF();
|
||||
executeTest("testMultipleSpanningDeletionsMD5", spec);
|
||||
}
|
||||
}
|
||||
|
|
@ -78,6 +78,7 @@ public class VariantContextMergerUnitTest extends BaseTest {
|
|||
Allele ATref;
|
||||
Allele Anoref;
|
||||
Allele GT;
|
||||
Allele del;
|
||||
|
||||
private GenomeLocParser genomeLocParser;
|
||||
|
||||
|
|
@ -94,6 +95,7 @@ public class VariantContextMergerUnitTest extends BaseTest {
|
|||
ATCATCT = Allele.create("ATCATCT");
|
||||
ATref = Allele.create("AT",true);
|
||||
Anoref = Allele.create("A",false);
|
||||
del = GATKVCFConstants.SPANNING_DELETION_SYMBOLIC_ALLELE;
|
||||
GT = Allele.create("GT",false);
|
||||
genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(hg18Reference)));
|
||||
}
|
||||
|
|
@ -217,6 +219,7 @@ public class VariantContextMergerUnitTest extends BaseTest {
|
|||
final List<Allele> AA_A_ALT = Arrays.asList(AAref, A, GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE);
|
||||
final Genotype gAA_A_ALT = new GenotypeBuilder("AA_A").PL(standardPLs).alleles(noCalls).make();
|
||||
final VariantContext vcAA_A_ALT = new VariantContextBuilder(VCprevBase).alleles(AA_A_ALT).genotypes(gAA_A_ALT).make();
|
||||
final List<Allele> A_C_del = Arrays.asList(Aref, C, del);
|
||||
|
||||
// first test the case of a single record
|
||||
tests.add(new Object[]{"test00",Arrays.asList(vcA_C_ALT),
|
||||
|
|
@ -249,18 +252,19 @@ public class VariantContextMergerUnitTest extends BaseTest {
|
|||
// a SNP with a spanning deletion
|
||||
tests.add(new Object[]{"test06",Arrays.asList(vcA_C_ALT, vcAA_A_ALT),
|
||||
loc, false, false,
|
||||
new VariantContextBuilder(VCbase).alleles(A_C).genotypes(gA_C, new GenotypeBuilder("AA_A").PL(new int[]{30, 71, 73}).alleles(noCalls).make()).make()});
|
||||
new VariantContextBuilder(VCbase).alleles(A_C_del).genotypes(new GenotypeBuilder("A_C").PL(new int[]{30, 20, 10, 71, 72, 73}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("AA_A").PL(new int[]{30, 71, 73, 20, 72, 10}).alleles(noCalls).make()).make()});
|
||||
|
||||
// combination of all
|
||||
tests.add(new Object[]{"test07",Arrays.asList(vcA_C_ALT, vcA_G_ALT, vcA_ATC_ALT, vcA_C_G_ALT, vcA_ALT, vcAA_ALT, vcAA_A_ALT),
|
||||
loc, false, false,
|
||||
new VariantContextBuilder(VCbase).alleles(Arrays.asList(Aref, C, G, ATC)).genotypes(new GenotypeBuilder("A_C").PL(new int[]{30, 20, 10, 71, 72, 73, 71, 72, 73, 73}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A_G").PL(new int[]{30, 71, 73, 20, 72, 10, 71, 73, 72, 73}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A_ATC").PL(new int[]{30, 71, 73, 71, 73, 73, 20, 72, 72, 10}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A_C_G").PL(new int[]{40,20,30,20,10,30,71,72,73,74}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A").PL(new int[]{0, 100, 1000, 100, 1000, 1000, 100, 1000, 1000, 1000}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("AA").PL(new int[]{0, 80, 800, 80, 800, 800, 80, 800, 800, 800}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("AA_A").PL(new int[]{30, 71, 73, 71, 73, 73, 71, 73, 73, 73}).alleles(noCalls).make()).make()});
|
||||
new VariantContextBuilder(VCbase).alleles(Arrays.asList(Aref, C, G, ATC, del)).genotypes(new GenotypeBuilder("A_C").PL(new int[]{30, 20, 10, 71, 72, 73, 71, 72, 73, 73, 71, 72, 73, 73, 73}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A_G").PL(new int[]{30, 71, 73, 20, 72, 10, 71, 73, 72, 73, 71, 73, 72, 73, 73}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A_ATC").PL(new int[]{30, 71, 73, 71, 73, 73, 20, 72, 72, 10, 71, 73, 73, 72, 73}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A_C_G").PL(new int[]{40, 20, 30, 20, 10, 30, 71, 72, 73, 74, 71, 72, 73, 74, 74}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("A").PL(new int[]{0, 100, 1000, 100, 1000, 1000, 100, 1000, 1000, 1000, 100, 1000, 1000, 1000, 1000}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("AA").PL(new int[]{0, 80, 800, 80, 800, 800, 80, 800, 800, 800, 80, 800, 800, 800, 800}).alleles(noCalls).make(),
|
||||
new GenotypeBuilder("AA_A").PL(new int[]{30, 71, 73, 71, 73, 73, 71, 73, 73, 73, 20, 72, 72, 72, 10}).alleles(noCalls).make()).make()});
|
||||
|
||||
// just spanning ref contexts, trying both instances where we want/do not want ref-only contexts
|
||||
tests.add(new Object[]{"test08",Arrays.asList(vcAA_ALT),
|
||||
|
|
|
|||
|
|
@ -123,7 +123,10 @@ public final class GATKVCFConstants {
|
|||
public static final String BEAGLE_MONO_FILTER_NAME = "BGL_SET_TO_MONOMORPHIC";
|
||||
public static final String LOW_QUAL_FILTER_NAME = "LowQual";
|
||||
|
||||
//Alleles
|
||||
// Symbolic alleles
|
||||
public final static String SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG = "ALT";
|
||||
public final static String NON_REF_SYMBOLIC_ALLELE_NAME = "NON_REF";
|
||||
public final static Allele NON_REF_SYMBOLIC_ALLELE = Allele.create("<"+NON_REF_SYMBOLIC_ALLELE_NAME+">", false); // represents any possible non-ref allele at this site
|
||||
public final static String SPANNING_DELETION_SYMBOLIC_ALLELE_NAME = "*:DEL";
|
||||
public final static Allele SPANNING_DELETION_SYMBOLIC_ALLELE = Allele.create("<"+SPANNING_DELETION_SYMBOLIC_ALLELE_NAME+">", false); // represents any possible spanning deletion allele at this site
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue