From bdf772f017e8ead76238648f76778591263a9de4 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 May 2009 20:35:08 +0000
Subject: [PATCH] Added test for determining the fraction of a sequence that's
 taken up by the most frequent base (quick-and-dirty homopolymer testing).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@780 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/BaseUtilsTest.java            | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100755 java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java

diff --git a/java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java b/java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java
new file mode 100755
index 000000000..9a0d17dc7
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java
@@ -0,0 +1,25 @@
+package org.broadinstitute.sting.utils;
+
+import org.broadinstitute.sting.BaseTest;
+import org.junit.Test;
+import org.junit.BeforeClass;
+import org.junit.Assert;
+
+public class BaseUtilsTest extends BaseTest {
+    @BeforeClass
+    public static void init() { }
+
+    @Test
+    public void testMostFrequentBaseFraction() {
+        logger.warn("Executing testMostFrequentBaseFraction");
+        
+        compareFrequentBaseFractionToExpected("AAAAA", 1.0);
+        compareFrequentBaseFractionToExpected("ACCG", 0.5);
+        compareFrequentBaseFractionToExpected("ACCCCTTTTG", 4.0/10.0);
+    }
+
+    private void compareFrequentBaseFractionToExpected(String sequence, double expected) {
+        double fraction = BaseUtils.mostFrequentBaseFraction(sequence.getBytes());
+        Assert.assertTrue(MathUtils.compareDoubles(fraction, expected) == 0);
+    }
+}