From f29cadd7e220e3a1f714c2001cb270eeb547fa2c Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sat, 14 Jul 2012 23:49:48 -0400
Subject: [PATCH] By default, don't quantize quals in BQSRv2

---
 .../sting/gatk/arguments/GATKArgumentCollection.java        | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 84e89e8ec..d865497cb 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -203,11 +203,11 @@ public class GATKArgumentCollection {
      * Turns on the base quantization module. It requires a recalibration report (-BQSR).
      *
      * A value of 0 here means "do not quantize".
-     * Any value greater than zero will be used to recalculate the quantization using this many levels.
-     * Negative values do nothing (i.e. quantize using the recalibration report's quantization level -- same as not providing this parameter at all)
+     * Any value greater than zero will be used to recalculate the quantization using that many levels.
+     * Negative values mean that we should quantize using the recalibration report's quantization level.
      */
     @Argument(fullName="quantize_quals", shortName = "qq", doc = "Quantize quality scores to a given number of levels.", required=false)
-    public int quantizationLevels = -1;
+    public int quantizationLevels = 0;
 
     /**
      * Turns off printing of the base insertion and base deletion tags when using the -BQSR argument.  Only the base substitution qualities will be produced.