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Fix for G: make sure to generate the genotype conformations in the grid for the target frequency when not using grid search for anything except the conformations 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4382 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-09-29 16:44:53 +00:00
parent 4556e3b273
commit 2d1265771f
1 changed files with 7 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
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@ -316,6 +316,13 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
}
public Pair<Integer, Double> getGenotype(int frequency, String sample) {
// it's possible that the genotype conformation hash wasn't initialized
if ( samplesToGenotypesPerAF.get(frequency) == null ) {
// confirm that the current frequency is the target one
if ( frequency != this.frequency )
throw new IllegalStateException("Attempting to retrieve genotypes from an uninitialized hash for frequency " + frequency + " (the hash is current standing at frequency " + this.frequency + ")");
recordGenotypes();
}
return samplesToGenotypesPerAF.get(frequency).get(sample);
}