Examples with SWPairwiseAlignment org.broadinstitute.hellbender.utils.smithwaterman.SWPairwiseAlignment used on opensource projects

Example 6 with SWPairwiseAlignment

use of org.broadinstitute.hellbender.utils.smithwaterman.SWPairwiseAlignment in project gatk by broadinstitute.

the class ReadThreadingGraph method generateCigarAgainstDownwardsReferencePath.

/**
     * Generates the CIGAR string from the Smith-Waterman alignment of the dangling path (where the
     * provided vertex is the sink) and the reference path.
     *
     * @param vertex   the sink of the dangling chain
     * @param pruneFactor  the prune factor to use in ignoring chain pieces
     * @return a SmithWaterman object which can be null if no proper alignment could be generated
     */
@VisibleForTesting
final DanglingChainMergeHelper generateCigarAgainstDownwardsReferencePath(final MultiDeBruijnVertex vertex, final int pruneFactor, final int minDanglingBranchLength) {
    // while heads can be 0, tails absolutely cannot
    final int minTailPathLength = Math.max(1, minDanglingBranchLength);
    // find the lowest common ancestor path between this vertex and the diverging master path if available
    final List<MultiDeBruijnVertex> altPath = findPathUpwardsToLowestCommonAncestor(vertex, pruneFactor);
    if (// add 1 to include the LCA
    altPath == null || isRefSource(altPath.get(0)) || altPath.size() < minTailPathLength + 1) {
        return null;
    }
    // now get the reference path from the LCA
    final List<MultiDeBruijnVertex> refPath = getReferencePath(altPath.get(0), TraversalDirection.downwards, Optional.ofNullable(incomingEdgeOf(altPath.get(1))));
    // create the Smith-Waterman strings to use
    final byte[] refBases = getBasesForPath(refPath, false);
    final byte[] altBases = getBasesForPath(altPath, false);
    // run Smith-Waterman to determine the best alignment (and remove trailing deletions since they aren't interesting)
    final SWPairwiseAlignment alignment = new SWPairwiseAlignment(refBases, altBases, SWPairwiseAlignment.STANDARD_NGS, SWPairwiseAlignment.OverhangStrategy.LEADING_INDEL);
    return new DanglingChainMergeHelper(altPath, refPath, altBases, refBases, AlignmentUtils.removeTrailingDeletions(alignment.getCigar()));
}

Example 7 with SWPairwiseAlignment

use of org.broadinstitute.hellbender.utils.smithwaterman.SWPairwiseAlignment in project gatk by broadinstitute.

the class ReadThreadingGraph method generateCigarAgainstUpwardsReferencePath.

/**
     * Generates the CIGAR string from the Smith-Waterman alignment of the dangling path (where the
     * provided vertex is the source) and the reference path.
     *
     * @param vertex   the source of the dangling head
     * @param pruneFactor  the prune factor to use in ignoring chain pieces
     * @return a SmithWaterman object which can be null if no proper alignment could be generated
     */
@VisibleForTesting
final DanglingChainMergeHelper generateCigarAgainstUpwardsReferencePath(final MultiDeBruijnVertex vertex, final int pruneFactor, final int minDanglingBranchLength) {
    // find the highest common descendant path between vertex and the reference source if available
    final List<MultiDeBruijnVertex> altPath = findPathDownwardsToHighestCommonDescendantOfReference(vertex, pruneFactor);
    if (// add 1 to include the LCA
    altPath == null || isRefSink(altPath.get(0)) || altPath.size() < minDanglingBranchLength + 1) {
        return null;
    }
    // now get the reference path from the LCA
    final List<MultiDeBruijnVertex> refPath = getReferencePath(altPath.get(0), TraversalDirection.upwards, Optional.empty());
    // create the Smith-Waterman strings to use
    final byte[] refBases = getBasesForPath(refPath, true);
    final byte[] altBases = getBasesForPath(altPath, true);
    // run Smith-Waterman to determine the best alignment (and remove trailing deletions since they aren't interesting)
    final SWPairwiseAlignment alignment = new SWPairwiseAlignment(refBases, altBases, SWPairwiseAlignment.STANDARD_NGS, SWPairwiseAlignment.OverhangStrategy.LEADING_INDEL);
    return new DanglingChainMergeHelper(altPath, refPath, altBases, refBases, AlignmentUtils.removeTrailingDeletions(alignment.getCigar()));
}