From 4fddac9f22335388c13ce4c1719a6c99f56354b3 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 14 Dec 2011 16:24:43 -0500
Subject: [PATCH] Updating busted integration tests

---
 .../gatk/walkers/genotyper/UnifiedGenotyperEngine.java     | 7 +++++--
 .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java | 4 ++--
 2 files changed, 7 insertions(+), 4 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 f185af0c3..7e5f388b2 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
@@ -817,7 +817,7 @@ public class UnifiedGenotyperEngine {
 
             // create the new likelihoods array from the alleles we are allowed to use
             final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
-            final double[] newLikelihoods;
+            double[] newLikelihoods;
             if ( likelihoodIndexesToUse == null ) {
                 newLikelihoods = originalLikelihoods;
             } else {
@@ -825,6 +825,9 @@ public class UnifiedGenotyperEngine {
                 int newIndex = 0;
                 for ( int oldIndex : likelihoodIndexesToUse )
                     newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
+
+                // might need to re-normalize
+                newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
             }
 
             // if there is no mass on the (new) likelihoods and we actually have alternate alleles, then just no-call the sample
@@ -846,7 +849,7 @@ public class UnifiedGenotyperEngine {
             if ( numNewAltAlleles == 0 )
                 attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
             else
-                attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, newLikelihoods);
+                attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(newLikelihoods));
             calls.add(new Genotype(sample, myAlleles, qual, null, attrs, false));
         }
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 4ae00431c..6041f80b8 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -129,8 +129,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testOutputParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
         e.put( "-sites_only", "44f3b5b40e6ad44486cddfdb7e0bfcd8" );
-        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "94e53320f14c5ff29d62f68d36b46fcd" );
-        e.put( "--output_mode EMIT_ALL_SITES", "73ad1cc41786b12c5f0e6f3e9ec2b728" );
+        e.put( "--output_mode EMIT_ALL_CONFIDENT_SITES", "274bd9d1b9c7857690fa5f0228ffc6d7" );
+        e.put( "--output_mode EMIT_ALL_SITES", "594c6d3c48bbc73289de7727d768644d" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(