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Minor optimization

This commit is contained in:
Eric Banks 2012-02-06 00:48:00 -05:00
parent 5343f8ba67
commit cef550903e
1 changed files with 2 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
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@ -73,10 +73,11 @@ public class TransmissionDisequilibriumTest extends InfoFieldAnnotation implemen
// for each pair of alleles, add the likelihoods // for each pair of alleles, add the likelihoods
int numAlleles = vc.getNAlleles(); int numAlleles = vc.getNAlleles();
for ( int allele1 = 0; allele1 < numAlleles; allele1++ ) { for ( int allele1 = 0; allele1 < numAlleles; allele1++ ) {
final int HOM1index = determineHomIndex(allele1, numAlleles);
for ( int allele2 = allele1 + 1; allele2 < numAlleles; allele2++ ) { for ( int allele2 = allele1 + 1; allele2 < numAlleles; allele2++ ) {
// TODO -- cache these for better performance // TODO -- cache these for better performance
final int HOM1index = determineHomIndex(allele1, numAlleles);
final int HETindex = HOM1index + (allele2 - allele1); final int HETindex = HOM1index + (allele2 - allele1);
final int HOM2index = determineHomIndex(allele2, numAlleles); final int HOM2index = determineHomIndex(allele2, numAlleles);