From 7ed120361d8341eb7a69a80133627abb50e498ff Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Fri, 12 Aug 2011 12:23:44 -0400
Subject: [PATCH] Fixed bug that required symbolic alleles to be padded with
 reference base and added integration test to test parsing and output of
 symbolic alleles

---
 .../sting/utils/exceptions/UserException.java |  2 +-
 .../utils/variantcontext/VariantContext.java  |  5 ++-
 .../CNV/SymbolicAllelesIntegrationTest.java   | 39 +++++++++++++++++++
 3 files changed, 44 insertions(+), 2 deletions(-)
 create mode 100644 public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java

diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index b3524c0d8..274c64f42 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -170,7 +170,7 @@ public class UserException extends ReviewedStingException {
         }
 
         public MalformedVCF(String message, int lineNo) {
-            super(String.format("The provided VCF file is malformed at line nmber %d: %s", lineNo, message));
+            super(String.format("The provided VCF file is malformed at line number %d: %s", lineNo, message));
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 23478cc2b..ca3399c78 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1209,7 +1209,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     }
 
     private void validateReferencePadding() {
-        boolean needsPadding = hasSymbolicAlleles() || (getReference().length() == getEnd() - getStart()); // off by one because padded base was removed
+        if (hasSymbolicAlleles()) // symbolic alleles don't need padding...
+            return;
+
+        boolean needsPadding = (getReference().length() == getEnd() - getStart()); // off by one because padded base was removed
 
         if ( needsPadding && !hasReferenceBaseForIndel() )
             throw new ReviewedStingException("Badly formed variant context at location " + getChr() + ":" + getStart() + "; no padded reference base was provided.");
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java
new file mode 100644
index 000000000..b4a8498e1
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java
@@ -0,0 +1,39 @@
+package org.broadinstitute.sting.gatk.walkers.CNV;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class SymbolicAllelesIntegrationTest extends WalkerTest {
+
+    public static String baseTestString(String reference, String VCF) {
+        return "-T CombineVariants" +
+                " -R " + reference +
+                " --variant:vcf " + validationDataLocation + VCF +
+                " -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED" +
+                " -genotypeMergeOptions REQUIRE_UNIQUE" +
+                " -setKey null" +
+                " -o %s" +
+                " -NO_HEADER";
+    }
+
+
+    @Test
+    public void test1() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(b36KGReference, "symbolic_alleles_1.vcf"),
+                1,
+                Arrays.asList("89a1c56f264ac27a2a4be81072473b6f"));
+        executeTest("Test symbolic alleles", spec);
+    }
+
+    @Test
+    public void test2() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
+                1,
+                Arrays.asList("6645babc8c7d46be0da223477c7b1291"));
+        executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
+    }
+}