From d84444200b364534d36fb0c4f76f41494cfd96f2 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 20 Nov 2009 16:13:18 +0000
Subject: [PATCH] The Unified Genotyper now sorts the sample names in the vcf
 that it outputs. [There was no reason to enforce that every VCF being output
 from the GATK should have the samples sorted, since someone might want them
 ordered non-alphabetically]

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2102 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java    | 4 ++--
 .../genotyper/UnifiedGenotyperIntegrationTest.java        | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 7751a0ab1..36f56c3e7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -62,7 +62,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
     private GenotypeWriter writer;
 
     // samples in input
-    private HashSet<String> samples;
+    private TreeSet<String> samples;
 
     // keep track of some metrics about our calls
     private CallMetrics callsMetrics;
@@ -108,7 +108,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<Genotype>, GenotypeL
         }
 
         // get all of the unique sample names
-        samples = new HashSet<String>();
+        samples = new TreeSet<String>();
         // if we're supposed to assume a single sample
         if ( UAC.ASSUME_SINGLE_SAMPLE != null ) {
             samples.add(UAC.ASSUME_SINGLE_SAMPLE);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index f30790853..4023fdb09 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1PointEM() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("37e112d619c2b6f213554edd10262523"));
+                Arrays.asList("fbb3ae6e835df5cf9b99dae5bf1fa8e5"));
         executeTest("testMultiSamplePilot1 - Point Estimate EM", spec);
     }
 
@@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot2PointEM() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("6d28b2af631805dc593508a21ef46a83"));
+                Arrays.asList("98495e6f75a63558996ed45f7a1f062a"));
         executeTest("testMultiSamplePilot2 - Point Estimate EM", spec);
     }
 
@@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("3a33873d7284cc113a639ee12c925ac0"));
+                Arrays.asList("6f2753dbbf6b4ff98a75510e7ff2d5ae"));
         executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
     }
 
@@ -76,7 +76,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot2Joint() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1,
-                Arrays.asList("bcdb54d8867543c5c316b65b27b0d3d6"));
+                Arrays.asList("979c1d88f2464548e83027daf685c2ad"));
         executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
     }