Examples with PileupElement org.broadinstitute.hellbender.utils.pileup.PileupElement used on opensource projects

Example 11 with PileupElement

use of org.broadinstitute.hellbender.utils.pileup.PileupElement in project gatk-protected by broadinstitute.

the class ReferenceConfidenceModel method calcNIndelInformativeReads.

/**
     * Calculate the number of indel informative reads at pileup
     *
     * @param pileup a pileup
     * @param pileupOffsetIntoRef the position of the pileup in the reference
     * @param ref the ref bases
     * @param maxIndelSize maximum indel size to consider in the informativeness calculation
     * @return an integer >= 0
     */
@VisibleForTesting
int calcNIndelInformativeReads(final ReadPileup pileup, final int pileupOffsetIntoRef, final byte[] ref, final int maxIndelSize) {
    int nInformative = 0;
    for (final PileupElement p : pileup) {
        final GATKRead read = p.getRead();
        final int offset = p.getOffset();
        // doesn't count as evidence
        if (p.isBeforeDeletionStart() || p.isBeforeInsertion() || p.isDeletion()) {
            continue;
        }
        // todo -- this code really should handle CIGARs directly instead of relying on the above tests
        if (isReadInformativeAboutIndelsOfSize(read, offset, ref, pileupOffsetIntoRef, maxIndelSize)) {
            nInformative++;
            if (nInformative > MAX_N_INDEL_INFORMATIVE_READS) {
                return MAX_N_INDEL_INFORMATIVE_READS;
            }
        }
    }
    return nInformative;
}

Example 12 with PileupElement

use of org.broadinstitute.hellbender.utils.pileup.PileupElement in project gatk-protected by broadinstitute.

the class ReferenceConfidenceModel method calcGenotypeLikelihoodsOfRefVsAny.

/**
     * Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs. alt
     *
     * @param ploidy target sample ploidy.
     * @param pileup the read backed pileup containing the data we want to evaluate
     * @param refBase the reference base at this pileup position
     * @param minBaseQual the min base quality for a read in the pileup at the pileup position to be included in the calculation
     * @param hqSoftClips running average data structure (can be null) to collect information about the number of high quality soft clips
     * @return a RefVsAnyResult genotype call.
     */
public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, final ReadPileup pileup, final byte refBase, final byte minBaseQual, final MathUtils.RunningAverage hqSoftClips) {
    final int likelihoodCount = ploidy + 1;
    final double log10Ploidy = MathUtils.log10(ploidy);
    final RefVsAnyResult result = new RefVsAnyResult(likelihoodCount);
    int readCount = 0;
    for (final PileupElement p : pileup) {
        final byte qual = p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual();
        if (!p.isDeletion() && qual <= minBaseQual) {
            continue;
        }
        readCount++;
        applyPileupElementRefVsNonRefLikelihoodAndCount(refBase, likelihoodCount, log10Ploidy, result, p, qual, hqSoftClips);
    }
    final double denominator = readCount * log10Ploidy;
    for (int i = 0; i < likelihoodCount; i++) {
        result.addGenotypeLikelihood(i, -denominator);
    }
    return result;
}

Example 13 with PileupElement

use of org.broadinstitute.hellbender.utils.pileup.PileupElement in project gatk by broadinstitute.

the class Pileup method createVerboseOutput.

/**
     * Collect information for the overlapping reads, delimited by {@link #VERBOSE_DELIMITER}
     * @param pileup the pileup to format
     * @return formatted string with read information for the pileup
     */
@VisibleForTesting
static String createVerboseOutput(final ReadPileup pileup) {
    final StringBuilder sb = new StringBuilder();
    boolean isFirst = true;
    sb.append(pileup.getNumberOfElements(PileupElement::isDeletion));
    sb.append(" ");
    for (final PileupElement p : pileup) {
        if (isFirst) {
            isFirst = false;
        } else {
            sb.append(",");
        }
        sb.append(p.getRead().getName());
        sb.append(VERBOSE_DELIMITER);
        sb.append(p.getOffset());
        sb.append(VERBOSE_DELIMITER);
        sb.append(p.getRead().getLength());
        sb.append(VERBOSE_DELIMITER);
        sb.append(p.getRead().getMappingQuality());
    }
    return sb.toString();
}

Example 14 with PileupElement

use of org.broadinstitute.hellbender.utils.pileup.PileupElement in project gatk by broadinstitute.

the class ReferenceConfidenceModel method calcGenotypeLikelihoodsOfRefVsAny.

/**
     * Calculate the genotype likelihoods for the sample in pileup for being hom-ref contrasted with being ref vs. alt
     *
     * @param ploidy target sample ploidy.
     * @param pileup the read backed pileup containing the data we want to evaluate
     * @param refBase the reference base at this pileup position
     * @param minBaseQual the min base quality for a read in the pileup at the pileup position to be included in the calculation
     * @param hqSoftClips running average data structure (can be null) to collect information about the number of high quality soft clips
     * @return a RefVsAnyResult genotype call.
     */
public RefVsAnyResult calcGenotypeLikelihoodsOfRefVsAny(final int ploidy, final ReadPileup pileup, final byte refBase, final byte minBaseQual, final MathUtils.RunningAverage hqSoftClips) {
    final int likelihoodCount = ploidy + 1;
    final double log10Ploidy = MathUtils.log10(ploidy);
    final RefVsAnyResult result = new RefVsAnyResult(likelihoodCount);
    int readCount = 0;
    for (final PileupElement p : pileup) {
        final byte qual = p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual();
        if (!p.isDeletion() && qual <= minBaseQual) {
            continue;
        }
        readCount++;
        applyPileupElementRefVsNonRefLikelihoodAndCount(refBase, likelihoodCount, log10Ploidy, result, p, qual, hqSoftClips);
    }
    final double denominator = readCount * log10Ploidy;
    for (int i = 0; i < likelihoodCount; i++) {
        result.addGenotypeLikelihood(i, -denominator);
    }
    return result;
}

Example 15 with PileupElement

use of org.broadinstitute.hellbender.utils.pileup.PileupElement in project gatk by broadinstitute.

the class LocusIteratorByState method lazyLoadNextAlignmentContext.

/**
     * Creates the next alignment context from the given state.  Note that this is implemented as a
     * lazy load method. nextAlignmentContext MUST BE null in order for this method to advance to the
     * next entry.
     */
private void lazyLoadNextAlignmentContext() {
    while (nextAlignmentContext == null && readStates.hasNext()) {
        readStates.collectPendingReads();
        final Locatable location = getLocation();
        final Map<String, ReadPileup> fullPileupPerSample = new LinkedHashMap<>();
        for (final Map.Entry<String, PerSampleReadStateManager> sampleStatePair : readStates) {
            final String sample = sampleStatePair.getKey();
            final PerSampleReadStateManager readState = sampleStatePair.getValue();
            final Iterator<AlignmentStateMachine> iterator = readState.iterator();
            final List<PileupElement> pile = new ArrayList<>(readState.size());
            while (iterator.hasNext()) {
                // state object with the read/offset information
                final AlignmentStateMachine state = iterator.next();
                final GATKRead read = state.getRead();
                final CigarOperator op = state.getCigarOperator();
                if (!includeReadsWithNsAtLoci && op == CigarOperator.N) {
                    continue;
                }
                if (!dontIncludeReadInPileup(read, location.getStart())) {
                    if (!includeReadsWithDeletionAtLoci && op == CigarOperator.D) {
                        continue;
                    }
                    pile.add(state.makePileupElement());
                }
            }
            if (!pile.isEmpty()) {
                // if this pileup added at least one base, add it to the full pileup
                fullPileupPerSample.put(sample, new ReadPileup(location, pile));
            }
        }
        // critical - must be called after we get the current state offsets and location
        readStates.updateReadStates();
        if (!fullPileupPerSample.isEmpty()) {
            // if we got reads with non-D/N over the current position, we are done
            nextAlignmentContext = new AlignmentContext(location, new ReadPileup(location, fullPileupPerSample));
        }
    }
}