public double likelihood() {
double c1 = 0.0;
double c3 = -1.0 / (double) Math.sqrt(2.0 * variance);
double sum = 0.0;
double cpart = -0.5 * Math.log(Math.sqrt(2.0 * Math.PI * variance));
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
c1 += cpart;
double pi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double gammai = gammas[t][k];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[k]] - zi;
sum += (err * err);
}
}
return c1 + c3 * sum;
}
public double error() {
double sum = 0.0;
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
double pi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double gammai = gammas[t][k];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = Math.abs(data.values(i)[channels[k]] - zi);
sum += err;
}
}
return sum;
}
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 ClusterLikelihoods(
ClusterData d, Integer[] chs, int[] five, int[] three, double v, double l) {
data = d;
channels = chs.clone();
gammas = new double[five.length][channels.length];
for (int t = 0; t < gammas.length; t++) {
for (int i = 0; i < gammas[t].length; i++) {
gammas[t][i] = 1.0;
}
}
transcripts = new TreeMap<Integer, Set<Integer>>();
fiveprime = five;
threeprime = three;
if (fiveprime.length != threeprime.length) {
String msg = String.format("%d != %d", fiveprime.length, threeprime.length);
throw new IllegalArgumentException(msg);
}
variance = v;
lambda = l;
for (int t = 0; t < fiveprime.length; t++) {
transcripts.put(t, new TreeSet<Integer>());
}
for (int i = 0; i < data.size(); i++) {
int loc = data.location(i);
for (int t = 0; t < fiveprime.length; t++) {
if (fiveprime[t] <= loc && threeprime[t] >= loc) {
transcripts.get(t).add(i);
}
}
}
}
public static ReadData[] copyReadData(
final ReadStructure rs, final IlluminaDataType[] dts, final ClusterData toCopy) {
boolean doBases = false;
boolean doQuals = false;
boolean doInts = false;
boolean doNoise = false;
for (final IlluminaDataType dt : dts) {
switch (dt) {
case BaseCalls:
doBases = true;
break;
case QualityScores:
doQuals = true;
break;
case RawIntensities:
doInts = true;
break;
case Noise:
doNoise = true;
break;
}
}
if (!doBases && !doQuals && !doInts && !doNoise) return null;
final ReadData rdToCopy = toCopy.getRead(0); // Only gonna be one read in this
final ReadData[] rds = new ReadData[rs.nonSkips.length()];
int index = 0;
int baseIndex = 0;
for (int i = 0; i < rs.descriptors.size(); i++) {
final ReadDescriptor readDesc = rs.descriptors.get(i);
if (readDesc.type != ReadType.S) {
final ReadData curRead = new ReadData(readDesc.type);
if (doBases) {
final byte[] bases =
Arrays.copyOfRange(rdToCopy.getBases(), baseIndex, baseIndex + readDesc.length);
curRead.setBases(bases);
}
if (doQuals) {
final byte[] quals =
Arrays.copyOfRange(rdToCopy.getQualities(), baseIndex, baseIndex + readDesc.length);
curRead.setQualities(quals);
}
if (doInts) {
final FourChannelIntensityData fcid =
copyIntensities(rdToCopy.getRawIntensities(), baseIndex, readDesc.length);
curRead.setRawIntensities(fcid);
}
if (doNoise) {
final FourChannelIntensityData fcid =
copyIntensities(rdToCopy.getNoise(), baseIndex, readDesc.length);
curRead.setNoise(fcid);
}
rds[index++] = curRead;
}
baseIndex += readDesc.length;
}
return rds;
}
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;
}
public double delta(int i, int t) {
int diff = threeprime[t] - data.location(i);
return diff >= 0 ? (double) diff : 0.0;
}