From 557da77a1acea5556e0a865081d972d0cd6452c8 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 3 May 2012 11:02:37 -0400
Subject: [PATCH] Don't compute QD if there is no QUAL; added integration test
 for this

---
 .../sting/gatk/walkers/annotator/QualByDepth.java      |  2 +-
 .../annotator/VariantAnnotatorIntegrationTest.java     | 10 +++++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 24a107235..51b834bd2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -29,7 +29,7 @@ import java.util.Map;
 public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
-        if ( stratifiedContexts.size() == 0 )
+        if ( !vc.hasLog10PError() || stratifiedContexts.size() == 0 )
             return null;
 
         final GenotypesContext genotypes = vc.getGenotypes();
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 80c50fd5f..2f0ef1a0e 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -54,7 +54,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
 
     @Test
     public void testNoAnnotsNotAsking2() {
-        // this genotype annotations in this file are actually out of order.  If you don't parse the genotypes
+        // the genotype annotations in this file are actually out of order.  If you don't parse the genotypes
         // they don't get reordered.  It's a good test of the genotype ordering system.
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
@@ -126,6 +126,14 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         executeTest("getting DB tag with HM3", spec);
     }
 
+    @Test
+    public void testNoQuals() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " --variant " + validationDataLocation + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + validationDataLocation + "noQual.vcf -A QualByDepth", 1,
+                Arrays.asList("e531c9f90c17f0f859cd1ac851a8edd8"));
+        executeTest("test file doesn't have QUALs", spec);
+    }
+
     @Test
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(