From a8a6c63a32237390faf65ec7f11915a87be54a67 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Apr 2009 22:06:15 +0000
Subject: [PATCH] A class with some static methods that aid the manipulation of
 quality scores and probabilities (including a method to compress a base and
 quality score into a byte for SAM output.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@271 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/QualityUtils.java             | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/utils/QualityUtils.java

diff --git a/java/src/org/broadinstitute/sting/utils/QualityUtils.java b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
new file mode 100755
index 000000000..7d0082ee1
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/utils/QualityUtils.java
@@ -0,0 +1,22 @@
+package org.broadinstitute.sting.utils;
+
+public class QualityUtils {
+    private QualityUtils() {}
+    
+    static public double qualToProb(byte qual) {
+        return 1.0 - Math.pow(10.0, ((double) qual)/-10.0);
+    }
+
+    static public byte probToQual(double prob) {
+        return (byte) Math.round(-10.0*Math.log10(1.0 - prob + 0.0001));
+    }
+
+    static public byte qualAndProbToCompressedQuality(int baseIndex, double prob) {
+        byte compressedQual = (byte) baseIndex;
+        byte cprob = (byte) (100.0*prob);
+        byte qualmask = (byte) 252;
+        compressedQual += ((cprob << 2) & qualmask);
+
+        return compressedQual;
+    }
+}