Package org.broad.igv.sam

Examples of org.broad.igv.sam.ReadMate

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        this.end = alignmentEnd;

        if (isPaired()) {
            String mateReferenceName = json.get("mateReferenceSequenceName").getAsString();
            String mateChr = genome == null ? mateReferenceName : genome.getChromosomeAlias(mateReferenceName);
            this.setMate(new ReadMate(mateChr,
                    json.get("matePosition").getAsInt() - 1,
                    (this.flags & MATE_STRAND_FLAG) != 0,
                    (this.flags & MATE_UNMAPPED_FLAG) != 0));
        }
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    private static boolean passFilter(Alignment alignment, boolean properPairs) {

         // For paired coverage, see if the alignment is properly paired, and if it is the "leftmost" alignment
        // (to prevent double-counting the pair).
        if(properPairs) {
            ReadMate mate = alignment.getMate();
            if(!alignment.isProperPair() || alignment.getMate() == null || alignment.getStart() > mate.getStart()) {
                return false;
            }
        }

        return alignment.isMapped()  && !alignment.isDuplicate() && !alignment.isVendorFailedRead();
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                (alignment.getFirstOfPairStrand() != Strand.NONE);

        // For paired coverage, see if the alignment is properly paired, and if it is the "leftmost" alignment
        // (to prevent double-counting the pair).
        if (pairedCoverage) {
            ReadMate mate = alignment.getMate();
            if (!alignment.isProperPair() || alignment.getMate() == null || alignment.getStart() > mate.getStart()) {
                return false;
            }
            if (Math.abs(alignment.getInferredInsertSize()) > 10000) {
                log.warn("Very large insert size: " + Math.abs(alignment.getInferredInsertSize()) +
                        " for read " + alignment.getReadName() + ".  Skipped.");
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                alignment.isProperPair() &&
                !alignment.isDuplicate() &&
                alignment.getMappingQuality() > 0 &&
                !alignment.isVendorFailedRead() &&
                alignment.getInferredInsertSize() > 0) {
            ReadMate mate = alignment.getMate();
            boolean mateMapped = mate != null && mate.isMapped();
            boolean sameChromosome = mateMapped && mate.getChr().equals(alignment.getChr());
            return mateMapped && sameChromosome;
        }
        return false;
    }
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Related Classes of org.broad.igv.sam.ReadMate

  • org.broad.igv.ga4gh.Ga4ghAlignment
  • org.broad.igv.tools.converters.BamToBed
  • org.broad.igv.tools.CoverageCounter
  • org.broad.igv.tools.PairedEndStats
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