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TODO optimization targets

This commit is contained in:
Mark DePristo 2011-12-12 14:46:45 -05:00
parent 3519a897c4
commit d03425df2f
1 changed files with 8 additions and 2 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -56,7 +56,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
private static final ArrayList<double[]> getGLs(GenotypesContext GLs) { private static final ArrayList<double[]> getGLs(GenotypesContext GLs) {
ArrayList<double[]> genotypeLikelihoods = new ArrayList<double[]>(); ArrayList<double[]> genotypeLikelihoods = new ArrayList<double[]>(); // TODO -- initialize with size of GLs
genotypeLikelihoods.add(new double[]{0.0,0.0,0.0}); // dummy genotypeLikelihoods.add(new double[]{0.0,0.0,0.0}); // dummy
for ( Genotype sample : GLs.iterateInSampleNameOrder() ) { for ( Genotype sample : GLs.iterateInSampleNameOrder() ) {
@ -364,7 +364,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
else { else {
// all possible likelihoods for a given cell from which to choose the max // all possible likelihoods for a given cell from which to choose the max
final int numPaths = set.ACsetIndexToPLIndex.size() + 1; final int numPaths = set.ACsetIndexToPLIndex.size() + 1;
final double[] log10ConformationLikelihoods = new double[numPaths]; final double[] log10ConformationLikelihoods = new double[numPaths]; // TODO can be created just once, since you initialize it
for ( int j = 1; j < set.log10Likelihoods.length; j++ ) { for ( int j = 1; j < set.log10Likelihoods.length; j++ ) {
final double[] gl = genotypeLikelihoods.get(j); final double[] gl = genotypeLikelihoods.get(j);
@ -372,6 +372,8 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// initialize // initialize
for ( int i = 0; i < numPaths; i++ ) for ( int i = 0; i < numPaths; i++ )
// TODO -- Arrays.fill?
// todo -- is this even necessary? Why not have as else below?
log10ConformationLikelihoods[i] = Double.NEGATIVE_INFINITY; log10ConformationLikelihoods[i] = Double.NEGATIVE_INFINITY;
// deal with the AA case first // deal with the AA case first
@ -417,6 +419,10 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
} }
private static double determineCoefficient(int PLindex, final int j, final int[] ACcounts, final int totalK) { private static double determineCoefficient(int PLindex, final int j, final int[] ACcounts, final int totalK) {
// todo -- arent' there a small number of fixed values that this function can adopt?
// todo -- at a minimum it'd be good to partially compute some of these in ACCounts for performance
// todo -- need to cache PLIndex -> two alleles, compute looping over each PLIndex. Note all other operations are efficient
// todo -- this can be computed once at the start of the all operations
// the closed form representation generalized for multiple alleles is as follows: // the closed form representation generalized for multiple alleles is as follows:
// AA: (2j - totalK) * (2j - totalK - 1) // AA: (2j - totalK) * (2j - totalK - 1)