From 4baeb5979fecc5aacbe7d6b3219d6867f740eba8 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 10 Mar 2011 03:08:56 +0000
Subject: [PATCH] It turns out that Math.log10() can return 0, which leads to
 QUALs being set to -0, which is off-spec.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5415 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java | 2 +-
 java/src/org/broadinstitute/sting/utils/QualityUtils.java       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 3f2c43c96..488c24fc0 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
 
 
-public class    UnifiedArgumentCollection {
+public class UnifiedArgumentCollection {
 
     // control the various models to be used
     @Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- SNP is the default option, while DINDEL is also available for calling indels.", required = false)
diff --git a/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index 272b47e01..a465825aa 100755
--- a/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -78,7 +78,7 @@ public class QualityUtils {
     }
 
     static public double phredScaleErrorRate(double errorRate) {
-        return -10.0*Math.log10(errorRate);
+        return Math.abs(-10.0*Math.log10(errorRate));
     }
 
     static public double lodToPhredScaleErrorRate(double lod) {