From 64c65c7751822bac6072866799c631efe48a4314 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 May 2009 16:50:31 +0000
Subject: [PATCH] New methods to generated compressed SQ quality elements in
 line with the SAM spec.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@699 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/QualityUtils.java             | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
index c06ba3b08..3c212cf7c 100755
--- a/java/src/org/broadinstitute/sting/utils/QualityUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -73,6 +73,18 @@ public class QualityUtils {
         return compressedQual;
     }
 
+    static public byte baseAndProbDiffToCompressedQuality(int baseIndex, double probdiff) {
+        byte compressedQual = 0;
+
+        compressedQual = (byte) baseIndex;
+
+        byte cprob = (byte) probdiff;
+        byte qualmask = (byte) 252;
+        compressedQual += ((cprob << 2) & qualmask);
+
+        return compressedQual;
+    }
+
     /**
      * From a compressed base, extract the base index (0:A, 1:C, 2:G, 3:T)
      *
@@ -98,6 +110,15 @@ public class QualityUtils {
         return ((double) x2)/100.0;
     }
 
+    static public double compressedQualityToProbDiff(byte compressedQual) {
+        // Because java natives are signed, extra care must be taken to avoid
+        // shifting a 1 into the sign bit in the implicit promotion of 2 to an int.
+        int x2 = ((int) compressedQual) & 0xff;
+        x2 = (x2 >>> 2);
+
+        return ((double) x2);
+    }
+
     /**
      * Return the complement of a base index.
      *