From 473b860312fb3df70d7e9baa9d421450640edcd6 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 17 Nov 2011 15:31:45 -0500
Subject: [PATCH] Major determinism fix for UG and RankSumTest

-- Now these routines all iterate in sample name order (genotypes.iterateInSampleNameOrder) so that the results of UG and the annotator do not depend on the particular order of samples we see for the exact model and the RankSumTest
---
 .../sting/gatk/walkers/annotator/RankSumTest.java         | 4 ++--
 .../gatk/walkers/genotyper/ExactAFCalculationModel.java   | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index ebf33496f..c5a2df1fd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -43,7 +43,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
 
         if (vc.isSNP() && vc.isBiallelic()) {
             // todo - no current support for multiallelic snps
-            for ( final Genotype genotype : genotypes ) {
+            for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
                 final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
                 if ( context == null ) {
                     continue;
@@ -53,7 +53,7 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements Standar
         }
         else if (vc.isIndel() || vc.isMixed()) {
 
-            for ( final Genotype genotype : genotypes ) {
+            for ( final Genotype genotype : genotypes.iterateInSampleNameOrder() ) {
                 final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
                 if ( context == null ) {
                     continue;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 980088305..a7240ae88 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -98,7 +98,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         ArrayList<double[]> genotypeLikelihoods = new ArrayList<double[]>();
 
         genotypeLikelihoods.add(new double[]{0.0,0.0,0.0}); // dummy
-        for ( Genotype sample : GLs ) {
+        for ( Genotype sample : GLs.iterateInSampleNameOrder() ) {
             if ( sample.hasLikelihoods() ) {
                 double[] gls = sample.getLikelihoods().getAsVector();
 
@@ -290,12 +290,12 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
         // todo = can't deal with optimal dynamic programming solution with multiallelic records
         if (SIMPLE_GREEDY_GENOTYPER || !vc.isBiallelic()) {
-            sampleIndices.addAll(GLs.getSampleNames());
+            sampleIndices.addAll(GLs.getSampleNamesOrderedByName());
             sampleIdx = GLs.size();
         }
         else {
 
-            for ( final Genotype genotype : GLs ) {
+            for ( final Genotype genotype : GLs.iterateInSampleNameOrder() ) {
                 if ( !genotype.hasLikelihoods() )
                     continue;
 
@@ -419,7 +419,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
         }
 
-        for ( final Genotype genotype : GLs ) {
+        for ( final Genotype genotype : GLs.iterateInSampleNameOrder() ) {
             if ( !genotype.hasLikelihoods() )
                 continue;
             Genotype g = GLs.get(genotype.getSampleName());