Examples with VariantContextDirectedEvidence au.edu.wehi.idsv.VariantContextDirectedEvidence used on opensource projects

Example 1 with VariantContextDirectedEvidence

use of au.edu.wehi.idsv.VariantContextDirectedEvidence in project gridss by PapenfussLab.

the class ComputeCoverage method initIntervalCoverageAccumulator.

private IntervalCoverageAccumulator initIntervalCoverageAccumulator() {
    SAMSequenceDictionary dictionary = getReference().getSequenceDictionary();
    if (VCF == null) {
        return new IntervalCoverageAccumulator(COVERAGE_METHOD, dictionary, BIN_SIZE, null);
    } else {
        try (VCFFileReader vcfReader = new VCFFileReader(VCF, false)) {
            try (CloseableIterator<VariantContext> it = vcfReader.iterator()) {
                GenomicProcessingContext pc = new GenomicProcessingContext(new FileSystemContext(TMP_DIR.get(0), MAX_RECORDS_IN_RAM), REFERENCE_SEQUENCE, getReference());
                Iterator<IdsvVariantContext> idsvIt = Iterators.transform(it, variant -> IdsvVariantContext.create(pc, null, variant));
                Iterator<VariantContextDirectedEvidence> bpit = Iterators.filter(idsvIt, VariantContextDirectedEvidence.class);
                return new IntervalCoverageAccumulator(COVERAGE_METHOD, dictionary, BIN_SIZE, bpit);
            }
        }
    }
}

Example 2 with VariantContextDirectedEvidence

use of au.edu.wehi.idsv.VariantContextDirectedEvidence in project gridss by PapenfussLab.

the class TruthAnnotator method annotate.

public VariantContextDirectedEvidence annotate(VariantContextDirectedEvidence variant) {
    BreakendSummary variantBreakend = variant.getBreakendSummary();
    BreakpointSummary variantBreakpoint = null;
    if (variantBreakend instanceof BreakpointSummary) {
        variantBreakpoint = (BreakpointSummary) variantBreakend;
        variantBreakend = variantBreakpoint.localBreakend();
    }
    HashSet<String> breakpointHits = Sets.newHashSet();
    HashSet<String> breakendHits = Sets.newHashSet();
    for (IdsvVariantContext truthVariant : truth) {
        if ((truthVariant.hasAttribute(VcfSvConstants.SV_TYPE_KEY) && truthVariant.getAttributeAsString(VcfSvConstants.SV_TYPE_KEY, "").equals("INS")) || (truthVariant.hasAttribute(VcfSvConstants.SV_TYPE_KEY) && truthVariant.getAttributeAsString(VcfSvConstants.SV_TYPE_KEY, "").equals("DEL"))) {
            int svLen = truthVariant.getAttributeAsInt(VcfSvConstants.SV_LENGTH_KEY, 0);
            int untemplatedSequence = 0;
            if (variant instanceof VariantContextDirectedEvidence) {
                untemplatedSequence = ((VariantContextDirectedEvidence) variant).getBreakendSequence().length;
            }
            // two breakpoints: forward & backward
            BreakendSummary truthBreakendStart = new BreakendSummary(truthVariant.getReferenceIndex(), BreakendDirection.Forward, truthVariant.getStart());
            int endOffset = Math.max(0, -truthVariant.getAttributeAsInt(VcfSvConstants.SV_LENGTH_KEY, 0));
            endOffset = truthVariant.getStart() + endOffset + 1;
            BreakendSummary truthBreakendEnd = new BreakendSummary(truthVariant.getReferenceIndex(), BreakendDirection.Backward, endOffset);
            BreakpointSummary truthBreakpoint = new BreakpointSummary(truthBreakendStart, truthBreakendEnd);
            if (matches(truthBreakpoint, variantBreakpoint, svLen, untemplatedSequence)) {
                breakpointHits.add(truthVariant.getID());
            } else if (matches(truthBreakpoint, variantBreakend, svLen, untemplatedSequence)) {
                breakendHits.add(truthVariant.getID());
            }
        } else {
            throw new RuntimeException(String.format("Matching of truth variant at %s:%d not yet implemented.", truthVariant.getContig(), truthVariant.getStart()));
        }
    }
    if (!breakpointHits.isEmpty() || !breakendHits.isEmpty()) {
        IdsvVariantContextBuilder builder = new IdsvVariantContextBuilder(processContext, variant);
        builder.attribute("TRUTH_MATCHES", Lists.newArrayList(breakpointHits));
        builder.attribute("TRUTH_MISREALIGN", Lists.newArrayList(breakendHits));
        return (VariantContextDirectedEvidence) builder.make();
    }
    return variant;
}