Package net.sf.samtools

Examples of net.sf.samtools.Cigar.numCigarElements()

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  public static void replaceHardClips(SAMRecord read) {
    Cigar cigar = read.getCigar();
   
    if (cigar.getCigarElements().size() > 0) {
      CigarElement firstElement = cigar.getCigarElement(0);
      CigarElement lastElement  = cigar.getCigarElement(cigar.numCigarElements()-1);
     
      if ((firstElement.getOperator() == CigarOperator.H) ||
        (lastElement.getOperator() == CigarOperator.H)) {
       
        Cigar newCigar = new Cigar();
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  public static void removeSoftClips(SAMRecord read) {
   
    Cigar cigar = read.getCigar();
   
    CigarElement firstElement = cigar.getCigarElement(0);
    CigarElement lastElement  = cigar.getCigarElement(cigar.numCigarElements()-1);
   
    if ((firstElement.getOperator() == CigarOperator.S) ||
      (lastElement.getOperator() == CigarOperator.S)) {
   
      Cigar newCigar = new Cigar();
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      for (int i=0; i<left.getCigar().numCigarElements()-1; i++) {
        leftElements.add(leftCigar.getCigarElement(i));
      }

      // Drop leading S on right side
      for (int i=1; i<rightCigar.numCigarElements(); i++) {
        rightElements.add(rightCigar.getCigarElement(i));
      }
     
      // Encountered in dream test data at: chr20  22137016.  Not clear how to interpret.
      if (rightElements.get(0).getOperator() == CigarOperator.INSERTION) {
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