Examples with KGeneAlignmentParameters com.milaboratory.mixcr.vdjaligners.KGeneAlignmentParameters used on opensource projects

Example 1 with KGeneAlignmentParameters

use of com.milaboratory.mixcr.vdjaligners.KGeneAlignmentParameters in project mixcr by milaboratory.

the class TargetMerger method merge.

@SuppressWarnings("unchecked")
public AlignedTarget merge(AlignedTarget targetLeft, AlignedTarget targetRight, int offset, OverlapType overlapType, int nMismatches) {
    if (offset < 0)
        return merge(targetRight, targetLeft, -offset, overlapType, nMismatches);
    final NSequenceWithQuality mergedTarget = merger.overlap(targetLeft.getTarget(), targetRight.getTarget(), offset);
    EnumMap<GeneType, VDJCHit[]> result = new EnumMap<>(GeneType.class);
    for (GeneType geneType : GeneType.VJC_REFERENCE) {
        final BatchAlignerWithBaseParameters bp = ((KGeneAlignmentParameters) alignerParameters.getGeneAlignerParameters(geneType)).getParameters();
        final VDJCHit[] leftHits = targetLeft.getAlignments().getHits(geneType);
        final VDJCHit[] rightHits = targetRight.getAlignments().getHits(geneType);
        GeneFeature alignedFeature = leftHits.length == 0 ? rightHits.length == 0 ? null : rightHits[0].getAlignedFeature() : leftHits[0].getAlignedFeature();
        Map<VDJCGeneId, HitMappingRecord> map = extractHitsMapping(targetLeft, targetRight, geneType);
        ArrayList<VDJCHit> resultingHits = new ArrayList<>();
        for (Map.Entry<VDJCGeneId, HitMappingRecord> mE : map.entrySet()) {
            final VDJCGene gene = mE.getValue().gene;
            Alignment<NucleotideSequence> mergedAl = merge(bp.getScoring(), extractBandedWidth(bp), mergedTarget.getSequence(), offset, mE.getValue().alignments[0], mE.getValue().alignments[1]);
            resultingHits.add(new VDJCHit(gene, mergedAl, alignedFeature));
        }
        Collections.sort(resultingHits);
        // final float relativeMinScore = extractRelativeMinScore(bp);
        // int threshold = (int) (resultingHits.size() > 0 ? resultingHits.get(0).getScore() * relativeMinScore : 0);
        // for (int i = resultingHits.size() - 1; i > 0; --i)
        // if (resultingHits.get(i).getScore() < threshold)
        // resultingHits.remove(i);
        result.put(geneType, resultingHits.toArray(new VDJCHit[resultingHits.size()]));
    }
    VDJCAlignments alignments = new VDJCAlignments(result, new NSequenceWithQuality[] { mergedTarget }, new SequenceHistory[] { new SequenceHistory.Merge(overlapType, targetLeft.getHistory(), targetRight.getHistory(), offset, nMismatches) }, VDJCAlignments.mergeOriginalReads(targetLeft.getAlignments(), targetRight.getAlignments()));
    AlignedTarget resultTarget = new AlignedTarget(alignments, 0);
    for (BPoint bPoint : BPoint.values()) {
        int leftPoint = targetLeft.getBPoint(bPoint);
        int rightPoint = targetRight.getBPoint(bPoint);
        if (leftPoint != -1 && rightPoint != -1)
            throw new IllegalArgumentException("Same bPoint defined in both input targets.");
        else if (leftPoint != -1)
            resultTarget = resultTarget.setBPoint(bPoint, leftPoint);
        else if (rightPoint != -1)
            resultTarget = resultTarget.setBPoint(bPoint, offset + rightPoint);
    }
    return resultTarget;
}