Helpful functions for converting a base (char) to a base index (A:0, C:1, G:2, T:3, alphabetical and consistent with Illumina conventions to minimize confusion.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@373 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/BaseUtils.java

@@ -0,0 +1,31 @@
+package org.broadinstitute.sting.utils;
+
+public class BaseUtils {
+    static public int simpleBaseToBaseIndex(char base) {
+        switch (base) {
+            case 'A':
+            case 'a': return 0;
+
+            case 'C':
+            case 'c': return 1;
+
+            case 'G':
+            case 'g': return 2;
+
+            case 'T':
+            case 't': return 3;
+
+            default: return -1;
+        }
+    }
+
+    static public char baseIndexToSimpleBase(int baseIndex) {
+        switch (baseIndex) {
+            case 0: return 'A';
+            case 1: return 'C';
+            case 2: return 'G';
+            case 3: return 'T';
+            default: return '.';
+        }
+    }
+}