From 578e7fa36deb0a7e072a941faabad3917ec0b8d0 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 16 Aug 2010 16:47:58 +0000
Subject: [PATCH] Don't output -0 as qual value in VariantRecalibrator.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4044 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java  | 2 +-
 .../VariantRecalibrationWalkersIntegrationTest.java             | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 01c10ab13..eb71a6e82 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -203,7 +203,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     final double pVar = theModel.evaluateVariant( vc );
 
                     final double lod = (Math.log10(totalPrior) + Math.log10(pVar)) - ((Math.log10(1.0 - totalPrior)) + Math.log10(1.0));
-                    variantDatum.qual = QUALITY_SCALE_FACTOR * QualityUtils.lodToPhredScaleErrorRate(lod);
+                    variantDatum.qual = Math.abs( QUALITY_SCALE_FACTOR * QualityUtils.lodToPhredScaleErrorRate(lod) );
 
                     mapList.add( variantDatum );
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
index 72f55f997..1987855f8 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
@@ -37,7 +37,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
     @Test
     public void testVariantRecalibrator() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "df4e6f55c714b68b13e47b61d4bd0cd5" );
+        e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "3c5a41567b60b777875d585a379eb231" );
         
         for ( Map.Entry<String, String> entry : e.entrySet() ) {
             String vcf = entry.getKey();