Intermediate version with banded pair HMM
This commit is contained in:
Guillermo del Angel
parent
9afccd11b1
commit
ceffefa6a6
|
|
@ -31,6 +31,7 @@ import net.sf.samtools.CigarOperator;
|
||||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||||
import org.broadinstitute.sting.utils.Haplotype;
|
import org.broadinstitute.sting.utils.Haplotype;
|
||||||
import org.broadinstitute.sting.utils.MathUtils;
|
import org.broadinstitute.sting.utils.MathUtils;
|
||||||
|
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||||
import org.broadinstitute.sting.utils.pileup.PileupElement;
|
import org.broadinstitute.sting.utils.pileup.PileupElement;
|
||||||
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
|
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
|
||||||
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
|
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
|
||||||
|
|
@ -38,6 +39,8 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
|
||||||
import org.broadinstitute.sting.utils.variantcontext.Allele;
|
import org.broadinstitute.sting.utils.variantcontext.Allele;
|
||||||
|
|
||||||
import java.io.File;
|
import java.io.File;
|
||||||
|
import java.io.FileWriter;
|
||||||
|
import java.io.PrintStream;
|
||||||
import java.util.Arrays;
|
import java.util.Arrays;
|
||||||
import java.util.HashMap;
|
import java.util.HashMap;
|
||||||
import java.util.LinkedHashMap;
|
import java.util.LinkedHashMap;
|
||||||
|
|
@ -478,6 +481,8 @@ public class PairHMMIndelErrorModel {
|
||||||
final int X_METRIC_LENGTH = readBases.length+1;
|
final int X_METRIC_LENGTH = readBases.length+1;
|
||||||
final int Y_METRIC_LENGTH = haplotypeBases.length+1;
|
final int Y_METRIC_LENGTH = haplotypeBases.length+1;
|
||||||
|
|
||||||
|
final int BWIDTH = 10;
|
||||||
|
|
||||||
// initialize path metric and traceback memories for likelihood computation
|
// initialize path metric and traceback memories for likelihood computation
|
||||||
double[][] matchMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
|
double[][] matchMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
|
||||||
double[][] XMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
|
double[][] XMetricArray = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
|
||||||
|
|
@ -507,6 +512,96 @@ public class PairHMMIndelErrorModel {
|
||||||
bestActionArrayY[0][j] = bestActionArrayM[0][j] = bestActionArrayX[0][j] = LEFT_GOTO_Y;
|
bestActionArrayY[0][j] = bestActionArrayM[0][j] = bestActionArrayX[0][j] = LEFT_GOTO_Y;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
final int numDiags = X_METRIC_LENGTH + Y_METRIC_LENGTH -1;
|
||||||
|
final int elemsInDiag = Math.min(X_METRIC_LENGTH, Y_METRIC_LENGTH);
|
||||||
|
|
||||||
|
int idxWithMaxElement = 0;
|
||||||
|
|
||||||
|
for (int diag=0; diag < numDiags; diag++) {
|
||||||
|
|
||||||
|
int indI = 0;
|
||||||
|
int indJ = diag;
|
||||||
|
if (diag >= Y_METRIC_LENGTH ) {
|
||||||
|
indI = diag-(Y_METRIC_LENGTH-1);
|
||||||
|
indJ = Y_METRIC_LENGTH-1;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
double maxElementInDiag = Double.NEGATIVE_INFINITY;
|
||||||
|
|
||||||
|
int idxLow = idxWithMaxElement - BWIDTH;
|
||||||
|
int idxHigh = idxWithMaxElement + BWIDTH;
|
||||||
|
|
||||||
|
if (idxLow < 0)
|
||||||
|
idxLow = 0;
|
||||||
|
|
||||||
|
if (idxHigh > elemsInDiag )
|
||||||
|
idxHigh = elemsInDiag;
|
||||||
|
|
||||||
|
|
||||||
|
// for each diagonal, compute max element, and center band around it for next diagonal.
|
||||||
|
//
|
||||||
|
// start point is idxOfMax-BWIDTH, end pt is idxMax+BWIDTH
|
||||||
|
|
||||||
|
for (int el = idxLow; el < idxHigh; el++) {
|
||||||
|
// first row and first column of all matrices had been pre-filled before
|
||||||
|
int im1 = indI -1;
|
||||||
|
int jm1 = indJ - 1;
|
||||||
|
if (indI > 0 && indJ > 0) {
|
||||||
|
// update current point
|
||||||
|
byte x = readBases[im1];
|
||||||
|
byte y = haplotypeBases[jm1];
|
||||||
|
byte qual = readQuals[im1];
|
||||||
|
|
||||||
|
double bestMetric = 0.0;
|
||||||
|
|
||||||
|
// compute metric for match/mismatch
|
||||||
|
// workaround for reads whose bases quality = 0,
|
||||||
|
if (qual < 1)
|
||||||
|
qual = 1;
|
||||||
|
|
||||||
|
if (qual > MAX_CACHED_QUAL)
|
||||||
|
qual = MAX_CACHED_QUAL;
|
||||||
|
|
||||||
|
double pBaseRead = (x == y)? baseMatchArray[(int)qual]:baseMismatchArray[(int)qual];
|
||||||
|
|
||||||
|
matchMetricArray[indI][indJ] = MathUtils.softMax(matchMetricArray[im1][jm1] + pBaseRead, XMetricArray[im1][jm1] + pBaseRead,
|
||||||
|
YMetricArray[im1][jm1] + pBaseRead);
|
||||||
|
|
||||||
|
c = currentGOP[jm1];
|
||||||
|
d = currentGCP[jm1];
|
||||||
|
if (indJ == Y_METRIC_LENGTH-1)
|
||||||
|
c = d = END_GAP_COST;
|
||||||
|
|
||||||
|
|
||||||
|
XMetricArray[indI][indJ] = MathUtils.softMax(matchMetricArray[im1][indJ] + c, XMetricArray[im1][indJ] + d);
|
||||||
|
|
||||||
|
// update Y array
|
||||||
|
//c = (indI==X_METRIC_LENGTH-1? END_GAP_COST: currentGOP[jm1]);
|
||||||
|
//d = (indI==X_METRIC_LENGTH-1? END_GAP_COST: currentGCP[jm1]);
|
||||||
|
c = currentGOP[jm1];
|
||||||
|
d = currentGCP[jm1];
|
||||||
|
if (indI == X_METRIC_LENGTH-1)
|
||||||
|
c = d = END_GAP_COST;
|
||||||
|
|
||||||
|
YMetricArray[indI][indJ] = MathUtils.softMax(matchMetricArray[indI][jm1] + c, YMetricArray[indI][jm1] + d);
|
||||||
|
bestMetric = MathUtils.softMax(matchMetricArray[indI][indJ], XMetricArray[indI][indJ], YMetricArray[indI][indJ]);
|
||||||
|
|
||||||
|
if (bestMetric > maxElementInDiag) {
|
||||||
|
maxElementInDiag = bestMetric;
|
||||||
|
idxWithMaxElement = el ;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
indI++;
|
||||||
|
if (indI >=X_METRIC_LENGTH )
|
||||||
|
break;
|
||||||
|
indJ--;
|
||||||
|
if (indJ < 0)
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
/*
|
||||||
for (int indI=1; indI < X_METRIC_LENGTH; indI++) {
|
for (int indI=1; indI < X_METRIC_LENGTH; indI++) {
|
||||||
int im1 = indI-1;
|
int im1 = indI-1;
|
||||||
for (int indJ=1; indJ < Y_METRIC_LENGTH; indJ++) {
|
for (int indJ=1; indJ < Y_METRIC_LENGTH; indJ++) {
|
||||||
|
|
@ -526,6 +621,8 @@ public class PairHMMIndelErrorModel {
|
||||||
if (qual > MAX_CACHED_QUAL)
|
if (qual > MAX_CACHED_QUAL)
|
||||||
qual = MAX_CACHED_QUAL;
|
qual = MAX_CACHED_QUAL;
|
||||||
|
|
||||||
|
//qual = 30;
|
||||||
|
|
||||||
double pBaseRead = (x == y)? baseMatchArray[(int)qual]:baseMismatchArray[(int)qual];
|
double pBaseRead = (x == y)? baseMatchArray[(int)qual]:baseMismatchArray[(int)qual];
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -613,78 +710,39 @@ public class PairHMMIndelErrorModel {
|
||||||
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
*/
|
||||||
double bestMetric;
|
double bestMetric;
|
||||||
double metrics[] = new double[3];
|
double metrics[] = new double[3];
|
||||||
int bestTable=0, bestI=X_METRIC_LENGTH - 1, bestJ=Y_METRIC_LENGTH - 1;
|
final int bestI=X_METRIC_LENGTH - 1, bestJ=Y_METRIC_LENGTH - 1;
|
||||||
metrics[MATCH_OFFSET] = matchMetricArray[bestI][bestJ];
|
metrics[MATCH_OFFSET] = matchMetricArray[bestI][bestJ];
|
||||||
metrics[X_OFFSET] = XMetricArray[bestI][bestJ];
|
metrics[X_OFFSET] = XMetricArray[bestI][bestJ];
|
||||||
metrics[Y_OFFSET] = YMetricArray[bestI][bestJ];
|
metrics[Y_OFFSET] = YMetricArray[bestI][bestJ];
|
||||||
if (doViterbi) {
|
bestMetric = MathUtils.softMax(metrics);
|
||||||
bestTable = MathUtils.maxElementIndex(metrics);
|
|
||||||
bestMetric = metrics[bestTable];
|
|
||||||
}
|
|
||||||
else
|
|
||||||
bestMetric = MathUtils.softMax(metrics);
|
|
||||||
|
|
||||||
// Do traceback (needed only for debugging!)
|
if (DEBUG) {
|
||||||
if (DEBUG && doViterbi) {
|
PrintStream outx, outy, outm;
|
||||||
|
double[][] sumMetrics = new double[X_METRIC_LENGTH][Y_METRIC_LENGTH];
|
||||||
|
try {
|
||||||
|
outx = new PrintStream("../../UGOptim/datax.txt");
|
||||||
|
outy = new PrintStream("../../UGOptim/datay.txt");
|
||||||
|
outm = new PrintStream("../../UGOptim/datam.txt");
|
||||||
|
|
||||||
int bestAction;
|
for (int indI=0; indI < X_METRIC_LENGTH; indI++) {
|
||||||
int i = bestI;
|
for (int indJ=0; indJ < Y_METRIC_LENGTH; indJ++) {
|
||||||
int j = bestJ;
|
metrics[MATCH_OFFSET] = matchMetricArray[indI][indJ];
|
||||||
|
metrics[X_OFFSET] = XMetricArray[indI][indJ];
|
||||||
|
metrics[Y_OFFSET] = YMetricArray[indI][indJ];
|
||||||
System.out.println("Affine gap NW");
|
sumMetrics[indI][indJ] = MathUtils.softMax(metrics);
|
||||||
|
outx.format("%4.1f ", metrics[X_OFFSET]);
|
||||||
|
outy.format("%4.1f ", metrics[Y_OFFSET]);
|
||||||
String haplotypeString = new String (haplotypeBases);
|
outm.format("%4.1f ", metrics[MATCH_OFFSET]);
|
||||||
String readString = new String(readBases);
|
}
|
||||||
|
outx.println(); outm.println();outy.println();
|
||||||
|
|
||||||
while (i >0 || j >0) {
|
|
||||||
if (bestTable == X_OFFSET) {
|
|
||||||
// insert gap in Y
|
|
||||||
haplotypeString = haplotypeString.substring(0,j)+"-"+haplotypeString.substring(j);
|
|
||||||
bestAction = bestActionArrayX[i][j];
|
|
||||||
}
|
}
|
||||||
else if (bestTable == Y_OFFSET) {
|
outm.close(); outx.close(); outy.close();
|
||||||
readString = readString.substring(0,i)+"-"+readString.substring(i);
|
} catch (java.io.IOException e) { throw new UserException("bla");}
|
||||||
bestAction = bestActionArrayY[i][j];
|
}
|
||||||
|
|
||||||
}
|
|
||||||
else {
|
|
||||||
bestAction = bestActionArrayM[i][j];
|
|
||||||
}
|
|
||||||
System.out.print(bestAction);
|
|
||||||
|
|
||||||
|
|
||||||
// bestAction contains action to take at next step
|
|
||||||
// encoding of bestAction: upper 2 bits = direction, lower 2 bits = next table
|
|
||||||
|
|
||||||
// bestTable and nextDirection for next step
|
|
||||||
bestTable = bestAction & 0x3;
|
|
||||||
int nextDirection = bestAction >> 2;
|
|
||||||
if (nextDirection == UP) {
|
|
||||||
i--;
|
|
||||||
} else if (nextDirection == LEFT) {
|
|
||||||
j--;
|
|
||||||
} else { // if (nextDirection == DIAG)
|
|
||||||
i--; j--;
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
System.out.println("\nAlignment: ");
|
|
||||||
System.out.println("R:"+readString);
|
|
||||||
System.out.println("H:"+haplotypeString);
|
|
||||||
System.out.println();
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
if (DEBUG)
|
if (DEBUG)
|
||||||
System.out.format("Likelihood: %5.4f\n", bestMetric);
|
System.out.format("Likelihood: %5.4f\n", bestMetric);
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue