From c5220c0822a58ddb93ee38dc959a9d02b487bb8c Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Apr 2009 20:52:17 +0000
Subject: [PATCH] Four-base probs are now decoded with the relevant method in
 QualityUtils

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@351 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/AlleleFrequencyWalker.java      | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
index 382e7f882..003b944cd 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
@@ -167,9 +167,9 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
                 //System.out.printf("SQ field (hex): %s\n", bytesToHexString(hex_quals));
                 //System.out.printf("SAM record: %s\n", read.format());
 
-                int hex_qual = hex_quals[offset];
-                int called2num = hex_qual & 0x3;
-                double qual2 = (double)(hex_qual >> 2) / 100.0;
+                byte hex_qual = hex_quals[offset];
+                int called2num = QualityUtils.compressedQualityToBaseIndex(hex_qual);
+                double qual2 = QualityUtils.compressedQualityToProb(hex_qual);
                 //System.out.printf("2ND %x %d %f\n", hex_qual, called2num, qual2);
                 quals[i][called2num] = qual2;