From c7a8dffa89efe2d08530e46cb0f061f0a887bba9 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 7 Jan 2010 19:27:15 +0000
Subject: [PATCH] Check for division by 0 in annotations

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2539 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/annotator/QualByDepth.java            | 5 ++++-
 .../sting/gatk/walkers/annotator/SpanningDeletions.java      | 2 +-
 .../concordance/CallsetConcordanceIntegrationTest.java       | 2 +-
 .../walkers/genotyper/UnifiedGenotyperIntegrationTest.java   | 4 ++--
 4 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 629194964..04ccac374 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -24,8 +24,11 @@ public class QualByDepth extends StandardVariantAnnotation {
             return null;
 
         //double QbyD = genotypeQualByDepth(ref.getBase(), genotypes, stratifiedContexts);
-        double QbyD = 10.0 * variation.getNegLog10PError() / (double)variationQualByDepth(ref.getBase(), genotypes, stratifiedContexts);
+        int qDepth = variationQualByDepth(ref.getBase(), genotypes, stratifiedContexts);
+        if ( qDepth == 0 )
+            return null;
 
+        double QbyD = 10.0 * variation.getNegLog10PError() / (double)qDepth;
         return String.format("%.2f", QbyD);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index 2faf52302..1348d3261 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -20,7 +20,7 @@ public class SpanningDeletions extends StandardVariantAnnotation {
             deletions += pileup.getNumberOfDeletions();
             depth += pileup.size();
         }
-        return String.format("%.2f", (double)deletions/(double)depth);
+        return String.format("%.2f", depth == 0 ? 0.0 : (double)deletions/(double)depth);
     }
 
     public String getKeyName() { return "Dels"; }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
index 2e5ed1687..772687dce 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
@@ -46,7 +46,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest {
     public void testComplex() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B set1,VCF," + validationDataLocation + "complexExample.vcf -B set2,VCF," + validationDataLocation + "complexExample.vcf -CT NWayVenn", 1,
-                Arrays.asList("8b72e557c0dd111738eaa69e9003fb3f"));
+                Arrays.asList("7bc72ec5f8b0fda5d59ebd2526b53e48"));
         executeTest("testComplex", spec);
     }
 }
\ No newline at end of file
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
index d216ef53f..82c726c73 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
@@ -98,8 +98,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testParameter() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "-genotype", "2a8b8d4da5ceed494e2210b15c2c3eb0" );
-        e.put( "-all_bases", "69b20ce7fc18f78011ee02b48a8d69aa" );
+        e.put( "-genotype", "b3161d019d467d5f9045d2f5d7203006" );
+        e.put( "-all_bases", "655c7b8ce2f794a055fa49962b5a6a79" );
         e.put( "--min_base_quality_score 26", "67175e0262e626d46aaf3bc8680cf888" );
         e.put( "--min_mapping_quality_score 26", "8edb24206529a7a344008280ab69cbb2" );
         e.put( "--max_mismatches_in_40bp_window 5", "870812ed23b2c656439dc1c8e6376f89" );