public static ClusterData makeCd(
final int lane,
final int tile,
final int xCoord,
final int yCoord,
final boolean pf,
final byte[] bases,
final byte[] qualities,
final String matchedBarcode) {
final ReadData rd = new ReadData();
rd.setBases(Arrays.copyOf(bases, bases.length));
rd.setQualities(Arrays.copyOf(qualities, bases.length));
rd.setReadType(
ReadType.T); // This will be ignored, as the cluster will be chopped up by ReadStructure
final ClusterData cd = new ClusterData(rd);
cd.setLane(lane);
cd.setTile(tile);
cd.setX(xCoord);
cd.setY(yCoord);
cd.setPf(pf);
cd.setMatchedBarcode(matchedBarcode);
return cd;
}
public static ClusterData selectiveCopyCd(
final ClusterData toCopy, final String readStructure, final IlluminaDataType... dataTypes) {
final ReadStructure rs = new ReadStructure(readStructure);
final ReadData[] rd = copyReadData(rs, dataTypes, toCopy);
final ClusterData cd = new ClusterData(rd);
cd.setTile(toCopy.getTile());
cd.setLane(toCopy.getLane());
for (final IlluminaDataType idt : dataTypes) {
switch (idt) {
case Position:
cd.setX(toCopy.getX());
cd.setY(toCopy.getY());
break;
case PF:
cd.setPf(toCopy.isPf());
break;
case Barcodes:
cd.setMatchedBarcode(toCopy.getMatchedBarcode());
break;
default:
break;
}
}
return cd;
}