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Minor fixups to GenotypeLikelihoods

This commit is contained in:
Eric Banks 2012-04-05 09:14:37 -04:00
parent 82cad97caf
commit 2c956efa53
1 changed files with 3 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -223,12 +223,12 @@ public class GenotypeLikelihoods {
/** /**
* The maximum number of alleles that we can represent as genotype likelihoods * The maximum number of alleles that we can represent as genotype likelihoods
*/ */
final static int MAX_ALLELES_THAT_CAN_BE_GENOTYPED = 500; final static int MAX_ALLELES_THAT_CAN_BE_GENOTYPED = 50;
/* /*
* a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles * a cache of the PL index to the 2 alleles it represents over all possible numbers of alternate alleles
*/ */
private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALLELES_THAT_CAN_BE_GENOTYPED); // start with data for 10 alternate alleles private final static GenotypeLikelihoodsAllelePair[] PLIndexToAlleleIndex = calculatePLcache(MAX_ALLELES_THAT_CAN_BE_GENOTYPED);
private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) { private static GenotypeLikelihoodsAllelePair[] calculatePLcache(final int altAlleles) {
final int numLikelihoods = calculateNumLikelihoods(1+altAlleles, 2); final int numLikelihoods = calculateNumLikelihoods(1+altAlleles, 2);
@ -259,7 +259,7 @@ public class GenotypeLikelihoods {
* only total number of alt allele counts in all chromosomes. * only total number of alt allele counts in all chromosomes.
* *
* For example, S(3,2) = 6: For alleles A,B,C, on a diploid organism we have six possible genotypes: * For example, S(3,2) = 6: For alleles A,B,C, on a diploid organism we have six possible genotypes:
* AA,AB,BB,AB,BC,CC. * AA,AB,BB,AC,BC,CC.
* Another way of expressing is with vector (#of A alleles, # of B alleles, # of C alleles) * Another way of expressing is with vector (#of A alleles, # of B alleles, # of C alleles)
* which is then, for ordering above, (2,0,0), (1,1,0), (0,2,0), (1,1,0), (0,1,1), (0,0,2) * which is then, for ordering above, (2,0,0), (1,1,0), (0,2,0), (1,1,0), (0,1,1), (0,0,2)
* In general, for P=2 (regular biallelic), then S(N,2) = N*(N+1)/2 * In general, for P=2 (regular biallelic), then S(N,2) = N*(N+1)/2