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No need for dummy GLs

This commit is contained in:
Eric Banks 2012-10-19 12:13:59 -04:00
parent f08e5a44da
commit f7bd4998fc
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
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@ -136,7 +136,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
likelihoodSums[i] = new LikelihoodSum(vc.getAlternateAllele(i));
// based on the GLs, find the alternate alleles with the most probability; sum the GLs for the most likely genotype
final ArrayList<double[]> GLs = getGLs(vc.getGenotypes(), true);
final ArrayList<double[]> GLs = getGLs(vc.getGenotypes(), false);
for ( final double[] likelihoods : GLs ) {
final int PLindexOfBestGL = MathUtils.maxElementIndex(likelihoods);