Examples with AlignedTarget com.milaboratory.mixcr.partialassembler.AlignedTarget used on opensource projects

Example 1 with AlignedTarget

use of com.milaboratory.mixcr.partialassembler.AlignedTarget in project mixcr by milaboratory.

the class VDJCAlignerPVFirst method process0.

@Override
protected VDJCAlignmentResult<PairedRead> process0(final PairedRead input) {
    Target[] targets = getTargets(input);
    // Creates helper classes for each PTarget
    PAlignmentHelper[] helpers = createInitialHelpers(targets);
    VDJCAlignmentResult<PairedRead> result = parameters.getAllowPartialAlignments() ? processPartial(input, helpers) : processStrict(input, helpers);
    // if sAligner == null (which means --no-merge option), no merge will be performed
    if (result.alignment != null && sAligner != null) {
        final VDJCAlignments alignment = result.alignment;
        final TargetMerger.TargetMergingResult mergeResult = alignmentsMerger.merge(new AlignedTarget(alignment, 0), new AlignedTarget(alignment, 1), false);
        if (mergeResult.failedDueInconsistentAlignments()) {
            GeneType geneType = mergeResult.getFailedMergedGeneType();
            int removeId = alignment.getBestHit(geneType).getAlignment(0).getScore() > alignment.getBestHit(geneType).getAlignment(1).getScore() ? 1 : 0;
            if (listener != null)
                listener.onTopHitSequenceConflict(input, alignment, geneType);
            return new VDJCAlignmentResult<>(input, alignment.removeBestHitAlignment(geneType, removeId));
        } else if (mergeResult.isSuccessful()) {
            assert mergeResult.isUsingAlignments();
            NSequenceWithQuality alignedTarget = mergeResult.getResult().getTarget();
            SingleRead sRead = new SingleReadImpl(input.getId(), alignedTarget, "");
            VDJCAlignmentResult<SingleRead> sResult = sAligner.process0(sRead);
            if (sResult.alignment == null)
                return result;
            VDJCAlignments sAlignment = sResult.alignment.setHistory(new SequenceHistory[] { new SequenceHistory.Merge(SequenceHistory.OverlapType.AlignmentOverlap, result.alignment.getHistory(0), result.alignment.getHistory(1), mergeResult.getOffset(), mergeResult.getMismatched()) }, new SequenceRead[] { input });
            if (listener != null)
                listener.onSuccessfulAlignmentOverlap(input, sAlignment);
            return new VDJCAlignmentResult<>(input, sAlignment);
        }
    }
    return result;
}