Package net.sf.cram.encoding.read_features

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

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      case D:
        features.add(new Deletion(zeroBasedPositionInRead + 1,
            cigarElementLength));
        break;
      case N:
        features.add(new RefSkip(zeroBasedPositionInRead + 1,
            cigarElementLength));
        break;
      case P:
        features.add(new Padding(zeroBasedPositionInRead + 1,
            cigarElementLength));
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          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);
            break;
          case InsertBase.operator:
            InsertBase ib = new InsertBase(pos, bc.readData());
            rf.add(ib);
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        case Deletion.operator:
          Deletion dv = (Deletion) f;
          dlc.writeData(dv.getLength());
          break;
        case RefSkip.operator:
          RefSkip rsv = (RefSkip) f;
          refSkipCodec.writeData(rsv.getLength());
          break;
        case InsertBase.operator:
          InsertBase ib = (InsertBase) f;
          bc.writeData(ib.getBase());
          break;
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Related Classes of net.sf.cram.encoding.read_features.RefSkip

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