From 9093de1132be1c5a7cc657c552299bceb1f67c33 Mon Sep 17 00:00:00 2001
From: Christopher Hartl <chartl@broadinstitute.org>
Date: Tue, 3 Jan 2012 15:58:51 -0500
Subject: [PATCH] Cleanup: remove code to calculate the MLE AC in the UGE.

---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 2159da6e6..34be88dbb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -401,11 +401,6 @@ public class UnifiedGenotyperEngine {
 
         // *** note that calculating strand bias involves overwriting data structures, so we do that last
         final HashMap<String, Object> attributes = new HashMap<String, Object>();
-        List<Integer> mlecounts = new ArrayList<Integer>(AFresult.log10AlleleFrequencyPosteriors.length);
-        for ( int i = 0; i < AFresult.log10AlleleFrequencyLikelihoods.length ; i++) {
-            mlecounts.add(MathUtils.maxElementIndex(AFresult.log10AlleleFrequencyLikelihoods[i]));
-        }
-        attributes.put("MLEAC",Utils.join(",",mlecounts));
 
         // if the site was downsampled, record that fact
         if ( !limitedContext && rawContext.hasPileupBeenDownsampled() )