Package net.sf.cram.encoding.read_features

Examples of net.sf.cram.encoding.read_features.Deletion

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      cigarElementLength = cigarElement.getLength();
      CigarOperator operator = cigarElement.getOperator();

      switch (operator) {
      case D:
        features.add(new Deletion(zeroBasedPositionInRead + 1,
            cigarElementLength));
        break;
      case N:
        features.add(new RefSkip(zeroBasedPositionInRead + 1,
            cigarElementLength));
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        SoftClip sc = (SoftClip) v;
        for (int i = 0; i < sc.getSequence().length; i++)
          bases[posInRead++ - 1] = sc.getSequence()[i];
        break;
      case Deletion.operator:
        Deletion dv = (Deletion) v;
        posInSeq += dv.getLength();
        break;
      case InsertBase.operator:
        InsertBase ib = (InsertBase) v;
        bases[posInRead++ - 1] = ib.getBase();
        break;
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            SoftClip fv = new SoftClip(pos,
                softClipCodec.readData());
            rf.add(fv);
            break;
          case Deletion.operator:
            Deletion dv = new Deletion(pos, dlc.readData());
            rf.add(dv);
            break;
          case RefSkip.operator:
            RefSkip rsv = new RefSkip(pos, refSkipCodec.readData());
            rf.add(rsv);
View Full Code Here
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        case SoftClip.operator:
          SoftClip fv = (SoftClip) f;
          softClipCodec.writeData(fv.getSequence());
          break;
        case Deletion.operator:
          Deletion dv = (Deletion) f;
          dlc.writeData(dv.getLength());
          break;
        case RefSkip.operator:
          RefSkip rsv = (RefSkip) f;
          refSkipCodec.writeData(rsv.getLength());
          break;
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            sv.setPosition(newPos);
            sv.setBaseChange(new BaseChange(random.nextInt(4)));
            record.getReadFeatures().add(sv);
            break;
          case Deletion.operator:
            Deletion dv = new Deletion();
            dv.setPosition(newPos);
            dv.setLength(random.nextInt(10));
            record.getReadFeatures().add(dv);
            break;
          case Insertion.operator:
            Insertion iv = new Insertion();
            iv.setPosition(newPos);
View Full Code Here
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Related Classes of net.sf.cram.encoding.read_features.Deletion

  • net.sf.cram.BLOCK_PROTO
  • net.sf.cram.CramNormalizer
  • net.sf.cram.encoding.Reader
  • net.sf.cram.encoding.Writer
  • net.sf.cram.Sam2CramRecordFactory
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