From 2d1265771fe3db62162aa5c645454418f2732490 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 29 Sep 2010 16:44:53 +0000
Subject: [PATCH] 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
---
 .../walkers/genotyper/AlleleFrequencyCalculationModel.java | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
index 1a8e9a5d2..dbdb60b6d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
@@ -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);
         }