From 736a857e82316642cc7bf1d5583b66eeca1d807c Mon Sep 17 00:00:00 2001
From: Valentin Ruano-Rubio <valentin@broadinstitute.org>
Date: Fri, 12 Dec 2014 00:01:33 -0500
Subject: [PATCH] Fixing CombineGVCFs that writes out the wrong REF allele

Story:
=====

  - https://www.pivotaltracker.com/story/show/83259038

Changes:
=======

  - Done minimal changes to make the fix after an arduous attempt to understand
    CombineGVCFs code.

Test:
====

  - Added a integration test to explicitly test for the bug.

  - Updated a md5 changes as the bug was actually affecting one of the existing
    integration tests.
---
 .../tools/walkers/variantutils/CombineGVCFs.java     |  9 +++------
 .../variantutils/CombineGVCFsIntegrationTest.java    | 12 +++++++++++-
 2 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
index b2c33de27..c0c73af67 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java
@@ -256,11 +256,8 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
      */
     private void endPreviousStates(final OverallState state, final int pos, final PositionalState startingStates, boolean atCurrentPosition) {
 
-        final byte refBase;
-        if (atCurrentPosition)
-            refBase = startingStates.refBases.length > 1 ? startingStates.refBases[1] : (byte)'N';
-        else
-            refBase = startingStates.refBases[0];
+        final byte refBase = startingStates.refBases[0];
+        final byte refNextBase = (atCurrentPosition) ? (startingStates.refBases.length > 1 ? startingStates.refBases[1] : (byte)'N' ): refBase;
 
         final List<VariantContext> stoppedVCs = new ArrayList<>(state.VCs.size());
 
@@ -300,7 +297,7 @@ public class CombineGVCFs extends RodWalker<CombineGVCFs.PositionalState, Combin
 
             vcfWriter.add(mergedVC);
             state.prevPos = gLoc;
-            state.refAfterPrevPos = refBase;
+            state.refAfterPrevPos = refNextBase;
         }
     }
 
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
index b98711a92..d0a979294 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java
@@ -203,10 +203,20 @@ public class CombineGVCFsIntegrationTest extends WalkerTest {
         executeTest("testBasepairResolutionOutput", spec);
     }
 
+    @Test
+    public void testWrongReferenceBaseBugFix() throws Exception {
+        final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf"
+                + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input2.vcf") + " -o %s --no_cmdline_in_header");
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("04fa9d6084e4b3a7ea2ebe5675561e2f"));
+        spec.disableShadowBCF();
+        executeTest("testWrongReferenceBaseBugFix",spec);
+
+    }
+
     @Test
     public void testBasepairResolutionInput() throws Exception {
         final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -o %s --no_cmdline_in_header -V " + privateTestDir + "gvcf.basepairResolution.vcf";
-        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("eb56760419b295651b6d54ba3ad18f52"));
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("d3b3f0c8d8f8ef09475306a7814ddd38"));
         spec.disableShadowBCF();
         executeTest("testBasepairResolutionInput", spec);
     }