Package htsjdk.samtools

Examples of htsjdk.samtools.Cigar.numCigarElements()

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    int getNumClippedBasesAtEnd(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);

        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
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    int getNumClippedBasesAtEnd(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);

        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
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    int getNumClippedBasesAtEnd(SAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);

        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
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        // left align the CIGAR
        Cigar newCigar = AlignmentUtils.leftAlignIndel(originalCigar, refSeq, originalIndel, 0, 0, true);

        // update if necessary and write
        if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) {
            int difference = originalIndex - newCigar.getCigarElement(0).getLength();
            VariantContext newVC = new VariantContextBuilder(vc).start(vc.getStart()-difference).stop(vc.getEnd()-difference).make();
            //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference));

            final int indelIndex = originalIndex-difference;
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    private int getNumClippedBasesAtEnd(final GATKSAMRecord read) {
        // compute total number of clipped bases (soft or hard clipped)
        // check for hard clips (never consider these bases):
        final Cigar c = read.getCigar();
        CigarElement last = c.getCigarElement(c.numCigarElements() - 1);

        int numEndClippedBases = 0;
        if (last.getOperator() == CigarOperator.H) {
            numEndClippedBases = last.getLength();
        }
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        final List<VariantContext> proposedEvents = new ArrayList<>();

        int alignmentPos = 0;

        for( int cigarIndex = 0; cigarIndex < cigar.numCigarElements(); cigarIndex++ ) {
            final CigarElement ce = cigar.getCigarElement(cigarIndex);
            final int elementLength = ce.getLength();
            switch( ce.getOperator() ) {
                case I:
                {
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        // left align the CIGAR
        Cigar newCigar = AlignmentUtils.leftAlignIndel(originalCigar, refSeq, originalIndel, 0, 0, true);

        // update if necessary and write
        if ( !newCigar.equals(originalCigar) && newCigar.numCigarElements() > 1 ) {
            int difference = originalIndex - newCigar.getCigarElement(0).getLength();
            VariantContext newVC = new VariantContextBuilder(vc).start(vc.getStart()-difference).stop(vc.getEnd()-difference).make();
            //System.out.println("Moving record from " + vc.getChr()+":"+vc.getStart() + " to " + vc.getChr()+":"+(vc.getStart()-difference));

            final int indelIndex = originalIndex-difference;
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