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Fixing up apparent source control/merge snafu: fix to correctly output PL ordering in multi-allelic sites by UG was only half-committed and hence not working. This completes fix

This commit is contained in:
Guillermo del Angel 2011-08-10 15:31:49 -04:00
parent 8072bd9831
commit 8325cb8c26
1 changed files with 13 additions and 13 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -239,8 +239,8 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// now with banding // now with banding
public int linearExactBanded(Map<String, Genotype> GLs, public int linearExactBanded(Map<String, Genotype> GLs,
double[] log10AlleleFrequencyPriors, double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors) { double[] log10AlleleFrequencyPosteriors) {
throw new NotImplementedException(); throw new NotImplementedException();
// final int numSamples = GLs.size(); // final int numSamples = GLs.size();
// final int numChr = 2*numSamples; // final int numChr = 2*numSamples;
@ -419,7 +419,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
/** /**
* Can be overridden by concrete subclasses * Can be overridden by concrete subclasses
* @param vc variant context with genotype likelihoods * @param vc variant context with genotype likelihoods
@ -517,10 +517,10 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
double qual = Double.NEGATIVE_INFINITY; double qual = Double.NEGATIVE_INFINITY;
double[] likelihoods = g.getLikelihoods().getAsVector(); double[] likelihoods = g.getLikelihoods().getAsVector();
/* System.out.format("Sample: %s GL:",sample); /* System.out.format("Sample: %s GL:",sample);
for (int i=0; i < likelihoods.length; i++) for (int i=0; i < likelihoods.length; i++)
System.out.format("%1.4f ",likelihoods[i]); System.out.format("%1.4f ",likelihoods[i]);
*/ */
for (int i=0; i < likelihoods.length; i++) { for (int i=0; i < likelihoods.length; i++) {
if (i==bestGTguess) if (i==bestGTguess)
@ -531,14 +531,14 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// qual contains now max(likelihoods[k]) for all k != bestGTguess // qual contains now max(likelihoods[k]) for all k != bestGTguess
qual = likelihoods[bestGTguess] - qual; qual = likelihoods[bestGTguess] - qual;
// likelihoods are stored row-wise in upper triangular matrix. IE // likelihoods are stored row-wise in lower triangular matrix. IE
// for 2 alleles they have ordering AA,AB,BB // for 2 alleles they have ordering AA,AB,BB
// for 3 alleles they are ordered AA,AB,AC,BB,BC,CC // for 3 alleles they are ordered AA,AB,BB,AC,BC,CC
// Get now alleles corresponding to best index // Get now alleles corresponding to best index
int kk=0; int kk=0;
boolean done = false; boolean done = false;
for (int i=0; i < vc.getNAlleles(); i++) { for (int j=0; j < vc.getNAlleles(); j++) {
for (int j=i; j < vc.getNAlleles(); j++){ for (int i=0; i <= j; i++){
if (kk++ == bestGTguess) { if (kk++ == bestGTguess) {
if (i==0) if (i==0)
myAlleles.add(vc.getReference()); myAlleles.add(vc.getReference());
@ -565,7 +565,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
double chosenGenotype = normalized[bestGTguess]; double chosenGenotype = normalized[bestGTguess];
qual = -1.0 * Math.log10(1.0 - chosenGenotype); qual = -1.0 * Math.log10(1.0 - chosenGenotype);
} }
//System.out.println(myAlleles.toString()); //System.out.println(myAlleles.toString());
calls.put(sample, new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false)); calls.put(sample, new Genotype(sample, myAlleles, qual, null, g.getAttributes(), false));
} }
@ -592,7 +592,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
for (int j=0; j <=numChr; j++) for (int j=0; j <=numChr; j++)
logYMatrix[i][j] = Double.NEGATIVE_INFINITY; logYMatrix[i][j] = Double.NEGATIVE_INFINITY;
//YMatrix[0][0] = 1.0; //YMatrix[0][0] = 1.0;
logYMatrix[0][0] = 0.0; logYMatrix[0][0] = 0.0;
int j=0; int j=0;