Examples with MalformedReadFilter org.broadinstitute.gatk.engine.filters.MalformedReadFilter used on opensource projects

Example 1 with MalformedReadFilter

use of org.broadinstitute.gatk.engine.filters.MalformedReadFilter in project jvarkit by lindenb.

the class SoftClipAnnotator method map.

public Integer map(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
    if (tracker == null)
        return 0;
    final Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
    if (VCs.isEmpty()) {
        return 0;
    }
    final Collection<ReadFilter> readFilters = super.getToolkit().getFilters();
    for (final VariantContext ctx : VCs) {
        int observed_genotypes = 0;
        int num_some_clipped_genotypes = 0;
        final List<Genotype> genotypes = new ArrayList<>(ctx.getNSamples());
        for (int i = 0; i < ctx.getNSamples(); ++i) {
            final Genotype g = ctx.getGenotype(i);
            if (!g.isCalled() || g.isNoCall() || g.isHomRef()) {
                genotypes.add(g);
                continue;
            }
            final List<SamReader> bamReaderForSample = this.sample2bam.get(g.getSampleName());
            if (bamReaderForSample.isEmpty()) {
                genotypes.add(g);
                continue;
            }
            observed_genotypes++;
            int numberOfClipsOverlapping = 0;
            for (final SamReader samReader : bamReaderForSample) {
                final SAMRecordIterator iter = samReader.query(ctx.getContig(), Math.max(0, ctx.getStart() - extend4clip), ctx.getEnd() + extend4clip, false);
                while (iter.hasNext()) {
                    final SAMRecord samRecord = iter.next();
                    if (samRecord.getReadUnmappedFlag() || samRecord.getCigar() == null || !samRecord.getContig().equals(ctx.getContig()) || samRecord.getUnclippedEnd() < ctx.getStart() || samRecord.getUnclippedStart() > ctx.getEnd() || samRecord.getReadGroup() == null || !g.getSampleName().equals(samRecord.getReadGroup().getSample()))
                        continue;
                    boolean ok = true;
                    for (final ReadFilter readFilter : readFilters) {
                        // this one cannot't be correctly initialized...
                        if (readFilter instanceof MalformedReadFilter)
                            continue;
                        if (readFilter.filterOut(samRecord)) {
                            ok = false;
                            break;
                        }
                    }
                    if (!ok)
                        continue;
                    int refPos = samRecord.getUnclippedStart();
                    for (final CigarElement ce : samRecord.getCigar()) {
                        if (ce.getOperator().consumesReferenceBases() || ce.getOperator().isClipping()) {
                            final int refEnd = refPos + ce.getLength();
                            if (!(ctx.getEnd() < refPos || refEnd < ctx.getStart())) {
                                // System.err.println("IN "+ce+" "+ctx.getStart()+"-"+ctx.getEnd()+" : "+refPos+"-"+refPos+ce.getLength());
                                if (ce.getOperator().equals(CigarOperator.S)) {
                                    ++numberOfClipsOverlapping;
                                }
                            }
                            refPos += ce.getLength();
                        }
                        if (refPos > ctx.getEnd())
                            break;
                    }
                }
                iter.close();
            }
            if (numberOfClipsOverlapping == 0) {
                genotypes.add(g);
            } else {
                GenotypeBuilder gb = new GenotypeBuilder(g);
                gb.attribute(numClipInGenotypeFormatHeaderLine.getID(), numberOfClipsOverlapping);
                genotypes.add(gb.make());
                num_some_clipped_genotypes++;
            }
        }
        if (num_some_clipped_genotypes == 0) {
            vcfWriter.add(ctx);
        } else {
            final VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            vcb.genotypes(genotypes);
            if (observed_genotypes == num_some_clipped_genotypes) {
                vcb.filter(this.filterHaveClipInVariant.getID());
            }
            vcfWriter.add(vcb.make());
        }
    }
    return VCs.size();
}