From 24b72334b3b30da8384f2ffcf03ab673502c2320 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Tue, 11 Oct 2011 11:32:27 -0400
Subject: [PATCH] UnifiedGenotyper now correctly initializes the
 VariantAnnotator engine.

This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.

Added an integration test to cover this case so that it doesn't break again.
---
 .../gatk/walkers/genotyper/UnifiedGenotyper.java     |  8 +++++++-
 .../genotyper/UnifiedGenotyperIntegrationTest.java   | 12 ++++++++++--
 2 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 428f97e2a..9fdf65015 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -214,7 +214,13 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
 
         // initialize the header
-        writer.writeHeader(new VCFHeader(getHeaderInfo(), samples)) ;
+        Set<VCFHeaderLine> headerInfo = getHeaderInfo();
+
+        // invoke initialize() method on each of the annotation classes, allowing them to add their own header lines
+        // and perform any necessary initialization/validation steps
+        annotationEngine.invokeAnnotationInitializationMethods(headerInfo);
+
+        writer.writeHeader(new VCFHeader(headerInfo, samples));
     }
 
     private Set<VCFHeaderLine> getHeaderInfo() {
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index 41496bdf1..7ef75ec53 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 import java.io.File;
@@ -285,6 +286,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     }
 
-
-
+    @Test
+    public void testSnpEffAnnotationRequestedWithoutRodBinding() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000 " +
+                "-A SnpEff",
+                1,
+                UserException.class);
+        executeTest("testSnpEffAnnotationRequestedWithoutRodBinding", spec);
+    }
 }