From 87e41c83c56b2f36bd95f8a1736c530d588446b0 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 14 Aug 2012 15:02:30 -0400
Subject: [PATCH] In AlleleCount stratification, check to make sure the AC (or
 MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User
 Error if it isn't.  Added a test for bad AC.

---
 .../varianteval/stratifications/AlleleCount.java  |  4 ++++
 .../varianteval/VariantEvalIntegrationTest.java   | 15 +++++++++++++++
 2 files changed, 19 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index 158f20b61..50c5526e4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -51,6 +51,10 @@ public class AlleleCount extends VariantStratifier {
                     AC = Math.max(AC, eval.getCalledChrCount(allele));
             }
 
+            // make sure that the AC isn't invalid
+            if ( AC > eval.getCalledChrCount() )
+                throw new UserException.MalformedVCF(String.format("The AC or MLEAC value (%d) at position %s:%d is larger than the possible called chromosome count (%d)", AC, eval.getChr(), eval.getStart(), eval.getCalledChrCount()));
+
             return Collections.singletonList((Object) AC);
         } else {
             return Collections.emptyList();
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
index 94e52c2b9..c92d6d4cf 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -585,6 +585,21 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         executeTest("testStandardIndelEval", spec);
     }
 
+    @Test
+    public void testBadACValue() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-eval " + privateTestDir + "vcfexample.withBadAC.vcf",
+                        "-noST -ST AlleleCount",
+                        "-noEV -EV VariantSummary"
+                ),
+                0,
+                UserException.class);
+        executeTest("testBadACValue", spec);
+    }
+
 
     @Test()
     public void testIncompatibleEvalAndStrat() {