From 71e8f47a6c29ab905eec927afb22b7b966beb442 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 7 May 2009 18:04:18 +0000
Subject: [PATCH] boundQual function for capping qual values

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@623 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/QualityUtils.java | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index f8f283bbd..c06ba3b08 100755
--- a/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -43,11 +43,15 @@ public class QualityUtils {
      */
     static public byte probToQual(double prob, double eps) {
         double lp = Math.round(-10.0*Math.log10(1.0 - prob + eps));
-        byte b = (byte) Math.min(lp, 63);
+        byte b = boundQual((int)lp);
         //System.out.printf("LP is %f, byte is %d%n", lp, b);
         return b;
     }
 
+    static public byte boundQual(int qual) {
+        return (byte) Math.min(qual, 63);        
+    }
+
     /**
      * Compress a base and a probability into a single byte so that it can be output in a SAMRecord's SQ field.
      * Note: the highest probability this function can encode is 64%, so this function should only never be used on the best base hypothesis.