From b33f804cdcfe7e3107a2cf553f30eed74d4da3d2 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 17 Dec 2012 16:38:10 -0500
Subject: [PATCH] Inline increment function in RecalDatum to avoid minor
 duplication of work and multiple synchronized method calls

---
 .../broadinstitute/sting/utils/recalibration/RecalDatum.java | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
index 31eb40d24..4cacc26c4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
@@ -248,8 +248,9 @@ public class RecalDatum {
     @Requires({"incObservations >= 0", "incMismatches >= 0"})
     @Ensures({"numObservations == old(numObservations) + incObservations", "numMismatches == old(numMismatches) + incMismatches"})
     public synchronized void increment(final double incObservations, final double incMismatches) {
-        incrementNumObservations(incObservations);
-        incrementNumMismatches(incMismatches);
+        numObservations += incObservations;
+        numMismatches += incMismatches;
+        empiricalQuality = UNINITIALIZED;
     }
 
     @Ensures({"numObservations == old(numObservations) + 1", "numMismatches >= old(numMismatches)"})