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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
This commit is contained in:
kiran 2009-05-21 20:35:08 +00:00
parent d61a5261c1
commit bdf772f017
1 changed files with 25 additions and 0 deletions
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25
java/test/org/broadinstitute/sting/utils/BaseUtilsTest.java 100755
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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);
}
}