Package net.sf.cram.encoding.read_features

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

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        sv.setRefernceBase(refBase);
        bases[posInRead++ - 1] = base;
        posInSeq++;
        break;
      case Insertion.operator:
        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];
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            sv.setCode(code);
            // sv.setBaseChange(new BaseChange(bsc.readData()));
            rf.add(sv);
            break;
          case Insertion.operator:
            Insertion iv = new Insertion(pos, inc.readData());
            rf.add(iv);
            break;
          case SoftClip.operator:
            SoftClip fv = new SoftClip(pos,
                softClipCodec.readData());
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          else
            bsc.writeData(sv.getCode());
          // bsc.writeData((byte) sv.getBaseChange().getChange());
          break;
        case Insertion.operator:
          Insertion iv = (Insertion) f;
          inc.writeData(iv.getSequence());
          break;
        case SoftClip.operator:
          SoftClip fv = (SoftClip) f;
          softClipCodec.writeData(fv.getSequence());
          break;
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            dv.setPosition(newPos);
            dv.setLength(random.nextInt(10));
            record.getReadFeatures().add(dv);
            break;
          case Insertion.operator:
            Insertion iv = new Insertion();
            iv.setPosition(newPos);
            byte[] seq = new byte[random.nextInt(10) + 1];
            for (int p = 0; p < seq.length; p++)
              seq[p] = "ACGT".getBytes()[random.nextInt(4)];
            iv.setSequence(seq);
            record.getReadFeatures().add(iv);
            break;
          case ReadBase.operator:
            ReadBase rb = new ReadBase(newPos,
                "ACGT".getBytes()[random.nextInt(4)],
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Related Classes of net.sf.cram.encoding.read_features.Insertion

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