From 344c3aeb1d89165afa75d3bce7c19df222fd10bf Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 3 Jul 2012 14:42:44 -0400
Subject: [PATCH] Cleanup from previous commit

---
 .../src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java  | 2 +-
 .../org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java
index 1ebf3941b..274b0f8bb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Datum.java
@@ -85,7 +85,7 @@ public class Datum {
     double empiricalQualDouble() {
         final double doubleMismatches = (double) (numMismatches + SMOOTHING_CONSTANT);
         final double doubleObservations = (double) (numObservations + SMOOTHING_CONSTANT);
-        double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
+        final double empiricalQual = -10 * Math.log10(doubleMismatches / doubleObservations);
         return Math.min(empiricalQual, (double) QualityUtils.MAX_RECALIBRATED_Q_SCORE);
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java
index 6dc5e70d1..9b00b1876 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalDatum.java
@@ -57,7 +57,8 @@ public class RecalDatum extends Datum {
     public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) {
         numObservations = _numObservations;
         numMismatches = _numMismatches;
-        estimatedQReported = QualityUtils.qualToErrorProb(reportedQuality);
+        estimatedQReported = reportedQuality;
+        empiricalQuality = UNINITIALIZED;
     }
 
     public RecalDatum(final RecalDatum copy) {