From 5f8a3f95efd335fee13fca7ed6608ca17f970d7f Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 25 Jun 2010 21:03:05 +0000
Subject: [PATCH] The GT field once again reigns supreme (it must be the first
 genotype field).  Thanks for the catch Eric.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3645 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/refdata/features/vcf4/VCF4Codec.java     |  4 ++--
 .../gatk/refdata/features/vcf4/VCF4UnitTest.java  | 15 ++++++++++++---
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
index 82921e6f4..1444d8ae5 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
@@ -425,8 +425,8 @@ public class VCF4Codec implements FeatureCodec {
                     if (i >= GTValueSplitSize)
                         gtAttributes.put(genotypeKeyArray[i],".");
                     else if (genotypeKeyArray[i].equals("GT"))
-                        if (genotypeAlleleLocation >= 0)
-                            throw new StingException("Saw two GT fields in record at position " + locAndAlleles.first);
+                        if (i != 0)
+                            throw new StingException("Saw GT at position " + i + ", it must be at the first position for genotypes. At location = " + locAndAlleles.first);
                         else
                             genotypeAlleleLocation = i;
                     else if (genotypeKeyArray[i].equals("GQ"))
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java
index 763087440..bd999067d 100644
--- a/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java
@@ -174,21 +174,30 @@ public class VCF4UnitTest extends BaseTest {
 
 
     // test too many info fields - NOT a valid test with validation turned off in the VCF4 reader
-    String twoManyInfoLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2;HH\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.";
+    String twoManyInfoLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2;HH\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:0,0";
     //@Test(expected=StingException.class)
     public void testCheckTooManyInfoFields() {
         TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
         testSetup.codec.decode(twoManyInfoLine);
     }
     // test a regular line
-    String regularLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.";
+    String regularLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;DP=14;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:0,0";
     @Test
     public void testCheckInfoValidation() {
         TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
         testSetup.codec.decode(regularLine);
     }
     // test too few info lines, we don't provide the DP in this line
-    String twoFewInfoLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t1|0:48:8:51,51\t1/1:43:5:.,.";
+    // test GT field in the incorrect position (!= 0)
+    String GTFieldInTheWrongPosition = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;AF=0.5;DB;H2\tGQ:DP:HQ:GT\t48:1:51,51:0|0\t48:8:51,51:0|0\t43:5:0,0:0|0";
+    @Test(expected=StingException.class)
+    public void testCheckGTFieldOrdering() {
+        TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);
+        testSetup.codec.decode(GTFieldInTheWrongPosition);
+    }
+    
+    // test too few info lines, we don't provide the DP in this line
+    String twoFewInfoLine = "20\t14370\trs6054257\tG\tA\t29\tPASS\tNS=3;AF=0.5;DB;H2\tGT:GQ:DP:HQ\t0|0:48:1:51,51\t0|0:48:1:51,51\t0|0:48:1:51,51";
     @Test
     public void testCheckTwoFewInfoValidation() {
         TestSetup testSetup = new TestSetup().invoke(vcfGenotypeFile);