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Added loads of comments for future reference

This commit is contained in:
Eric Banks 2011-12-03 23:54:42 -05:00
parent 29662be3d7
commit eab2b76c9b
1 changed files with 22 additions and 8 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
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@ -284,11 +284,21 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// This class represents a column in the Exact AC calculation matrix
private static final class ExactACset {
// the counts of the various alternate alleles which this column represents
final int[] ACcounts;
// the column of the matrix
final double[] log10Likelihoods;
// mapping of column index for those columns upon which this one depends to the index into the PLs which is used as the transition to this column;
// for example, in the biallelic case, the transition from k=0 to k=1 would be AB while the transition to k=2 would be BB.
final HashMap<Integer, Integer> ACsetIndexToPLIndex = new HashMap<Integer, Integer>();
// to minimize memory consumption, we know we can delete any sets in this list because no further sets will depend on them
final ArrayList<Integer> dependentACsetsToDelete = new ArrayList<Integer>();
// index used to represent this set in the global hashmap: (numSamples^0 * allele_1) + (numSamples^1 * allele_2) + (numSamples^2 * allele_3) + ...
private int index = -1;
public ExactACset(int size, int[] ACcounts) {
@ -309,6 +319,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
return index;
}
// sum of all the non-reference alleles
public int getACsum() {
int sum = 0;
for ( int count : ACcounts )
@ -361,8 +372,8 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
final boolean preserveData,
final Queue<ExactACset> ACqueue,
final HashMap<Integer, ExactACset> indexesToACset,
double[] log10AlleleFrequencyPriors,
double[] log10AlleleFrequencyPosteriors) {
final double[] log10AlleleFrequencyPriors,
final double[] log10AlleleFrequencyPosteriors) {
// compute the log10Likelihoods
computeLofK(set, genotypeLikelihoods, indexesToACset, log10AlleleFrequencyPosteriors, log10AlleleFrequencyPriors);
@ -383,16 +394,16 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
// iterate over higher frequencies if possible
int ACwiggle = numChr - set.getACsum();
if ( ACwiggle == 0 ) // all alternate alleles already sum to 2N
if ( ACwiggle == 0 ) // all alternate alleles already sum to 2N so we cannot possibly go to higher frequencies
return log10LofK;
ExactACset lastSet = null;
ExactACset lastSet = null; // keep track of the last set placed in the queue so that we can tell it to clean us up when done processing
int numAltAlleles = set.ACcounts.length;
// genotype log10Likelihoods are a linear vector that can be thought of as a row-wise upper triangular matrix of log10Likelihoods.
// So e.g. with 2 alt alleles the log10Likelihoods are AA,AB,AC,BB,BC,CC and with 3 alt alleles they are AA,AB,AC,AD,BB,BC,BD,CC,CD,DD.
// genotype likelihoods are a linear vector that can be thought of as a row-wise upper triangular matrix of log10Likelihoods.
// so e.g. with 2 alt alleles the likelihoods are AA,AB,AC,BB,BC,CC and with 3 alt alleles they are AA,AB,AC,AD,BB,BC,BD,CC,CD,DD.
// do it for the k+1 case
// add conformations for the k+1 case
int PLindex = 0;
for ( int allele = 0; allele < numAltAlleles; allele++ ) {
int[] ACcountsClone = set.ACcounts.clone();
@ -400,7 +411,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
lastSet = updateACset(ACcountsClone, numChr, set.getIndex(), ++PLindex, ACqueue, indexesToACset);
}
// do it for the k+2 case if it makes sense; note that the 2 alleles may be the same or different
// add conformations for the k+2 case if it makes sense; note that the 2 new alleles may be the same or different
if ( ACwiggle > 1 ) {
for ( int allele_i = 0; allele_i < numAltAlleles; allele_i++ ) {
for ( int allele_j = allele_i; allele_j < numAltAlleles; allele_j++ ) {
@ -419,6 +430,8 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
return log10LofK;
}
// adds the ExactACset represented by the ACcounts to the ACqueue if not already there (creating it if needed) and
// also adds it as a dependency to the given callingSetIndex.
private static ExactACset updateACset(int[] ACcounts,
int numChr,
final int callingSetIndex,
@ -462,6 +475,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
final double[] gl = genotypeLikelihoods.get(j);
final double logDenominator = MathUtils.log10Cache[2*j] + MathUtils.log10Cache[2*j-1];
// initialize
for ( int i = 0; i < numPaths; i++ )
log10ConformationLikelihoods[i] = Double.NEGATIVE_INFINITY;