Package net.sf.cram.encoding.read_features

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

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      byte[] scores) {
    byte[] insertedBases = Arrays.copyOfRange(bases,
        zeroBasedPositionInRead, zeroBasedPositionInRead
            + cigarElementLength);

    SoftClip v = new SoftClip(zeroBasedPositionInRead + 1, insertedBases);
    features.add(v);
  }
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        Insertion iv = (Insertion) v;
        for (int i = 0; i < iv.getSequence().length; i++)
          bases[posInRead++ - 1] = iv.getSequence()[i];
        break;
      case SoftClip.operator:
        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;
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          case Insertion.operator:
            Insertion iv = new Insertion(pos, inc.readData());
            rf.add(iv);
            break;
          case SoftClip.operator:
            SoftClip fv = new SoftClip(pos,
                softClipCodec.readData());
            rf.add(fv);
            break;
          case Deletion.operator:
            Deletion dv = new Deletion(pos, dlc.readData());
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        case Insertion.operator:
          Insertion iv = (Insertion) f;
          inc.writeData(iv.getSequence());
          break;
        case SoftClip.operator:
          SoftClip fv = (SoftClip) f;
          softClipCodec.writeData(fv.getSequence());
          break;
        case Deletion.operator:
          Deletion dv = (Deletion) f;
          dlc.writeData(dv.getLength());
          break;
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Related Classes of net.sf.cram.encoding.read_features.SoftClip

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