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Don't initialize the cell conformation values (use an else in the loop instead) as per Mark's TODO

This commit is contained in:
Eric Banks 2012-01-12 08:50:03 -05:00
parent 410a340ef5
commit f5f5ed5dcd
1 changed files with 10 additions and 11 deletions
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21
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -324,12 +324,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// all possible likelihoods for a given cell from which to choose the max
final int numPaths = set.ACsetIndexToPLIndex.size() + 1;
final double[][] log10ConformationLikelihoods = new double[set.log10Likelihoods.length][numPaths]; // TODO can be created just once, since you initialize it
// initialize
for ( int i = 0; i < set.log10Likelihoods.length; i++ )
for ( int j = 0; j < numPaths; j++ )
// TODO -- Arrays.fill?
// todo -- is this even necessary? Why not have as else below?
log10ConformationLikelihoods[i][j] = Double.NEGATIVE_INFINITY;
// deal with the non-AA possible conformations
int conformationIndex = 1;
@ -340,12 +334,14 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
ExactACset dependent = indexesToACset.get(mapping.getKey());
for ( int j = 1; j < set.log10Likelihoods.length; j++ ) {
final double[] gl = genotypeLikelihoods.get(j);
if ( totalK <= 2*j ) { // skip impossible conformations
log10ConformationLikelihoods[j][conformationIndex] =
final double[] gl = genotypeLikelihoods.get(j);
log10ConformationLikelihoods[j][conformationIndex] =
determineCoefficient(mapping.getValue(), j, set.ACcounts.getCounts(), totalK) + dependent.log10Likelihoods[j-1] + gl[mapping.getValue()];
}
} else {
log10ConformationLikelihoods[j][conformationIndex] = Double.NEGATIVE_INFINITY;
}
}
conformationIndex++;
@ -353,10 +349,13 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// finally, deal with the AA case (which depends on previous cells in this column) and then update the L(j,k) value
for ( int j = 1; j < set.log10Likelihoods.length; j++ ) {
final double[] gl = genotypeLikelihoods.get(j);
if ( totalK < 2*j-1 )
if ( totalK < 2*j-1 ) {
final double[] gl = genotypeLikelihoods.get(j);
log10ConformationLikelihoods[j][0] = MathUtils.log10Cache[2*j-totalK] + MathUtils.log10Cache[2*j-totalK-1] + set.log10Likelihoods[j-1] + gl[HOM_REF_INDEX];
} else {
log10ConformationLikelihoods[j][0] = Double.NEGATIVE_INFINITY;
}
final double logDenominator = MathUtils.log10Cache[2*j] + MathUtils.log10Cache[2*j-1];
final double log10Max = MathUtils.approximateLog10SumLog10(log10ConformationLikelihoods[j]);