From 1f3624d2046738a0a8f827489e49b6a8282c7477 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 7 May 2013 11:59:18 -0400
Subject: [PATCH] Base Recalibrator doesn't recalibrate all reads, so the final
 output line was confusing

---
 .../sting/gatk/walkers/bqsr/BaseRecalibrator.java               | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
index dde49b7db..278317da3 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
@@ -519,7 +519,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
             generatePlots();
         }
 
-        logger.info("Processed: " + result + " reads");
+        logger.info("BaseRecalibrator was able to recalibrate " + result + " reads");
     }
 
     private RecalibrationTables getRecalibrationTable() {