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Cleaning up playground utils and tests 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4136 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-08-27 01:25:47 +00:00
parent 4979dcc9a7
commit bfcac33e80
2 changed files with 0 additions and 75 deletions
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java/src/org/broadinstitute/sting/playground/utils/PoolUtils.java → archive/java/src/org/broadinstitute/sting/poolseq/PoolUtils.java
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java/test/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerUnitTest.java
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package org.broadinstitute.sting.playground.gatk.walkers.poolseq;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.junit.Test;
import org.junit.Assert;
import java.math.BigDecimal;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Dec 14, 2009
* Time: 10:19:53 AM
* To change this template use File | Settings | File Templates.
*/
public class PowerUnitTest extends BaseTest {
// test for various items involved in PowerBelowFrequency
@Test
public void testBinomialProbabilityLog() {
logger.warn("Testing binomial probability in log space");
Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbabilityLog(5,7,0.3),0.02500,1e-4)==0);
Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbabilityLog(8000,15000,0.6),2.56e-62,1e-64) == 0);
Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbabilityLog(12000,20000,0.5),7.34e-178,1e-180) == 0);
Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbabilityLog(600,800,0.75),0.0326,0.0001) == 0);
Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbabilityLog(50,500,0.2),6.404e-10,1e-13)==0);
Assert.assertTrue(MathUtils.compareDoubles(MathUtils.binomialProbabilityLog(5277,8279,0.60344),1.6023145e-11,1e-18) == 0);
}
@Test
public void testBinomialCDF() {
logger.warn("Testing binomial CDF");
double test1 = MathUtils.cumBinomialProbLog(0,5277,8279,0.64344);
System.out.println("Binomial CDF -- Test 1: "+test1);
Assert.assertTrue(MathUtils.compareDoubles(test1,0.127,5e-3) == 0);
double test2 = MathUtils.cumBinomialProbLog(0,1472,9886,0.172);
System.out.println("Binomial CDF -- Test 2: "+test2);
Assert.assertTrue(MathUtils.compareDoubles(test2,3.1e-10,5e-11)==0);
double test3 = MathUtils.cumBinomialProbLog(0,1472,9886,0.142);
System.out.println("Binomial CDF -- Test 3: "+test3);
Assert.assertTrue(MathUtils.compareDoubles(test3,0.975,5e-3)==0);
double test4 = MathUtils.cumBinomialProbLog(0,6781,21297,0.321742);
System.out.println("Binomial CDF -- Test 4:"+test4);
Assert.assertTrue(MathUtils.compareDoubles(test4,0.150,5e-3)==0);
double test5 = MathUtils.cumBinomialProbLog(0,10609,21297,0.5001);
System.out.println("Binomial CDF == Test 5:"+test5);
Assert.assertTrue(MathUtils.compareDoubles(test5,0.286,5e-3)==0);
}
/* @Test
public void testPowerCalculation() {
PowerBelowFrequencyWalker w = new PowerBelowFrequencyWalker();
w.initialize();
logger.warn("Testing power on pool of 100 people");
w.setPoolSize(100);
// TEST 1
double error = 0.000123;
byte q = QualityUtils.probToQual(1-error);
double pow = w.theoreticalPower(1000,q,1,5);
System.out.println("Qual for "+error+"="+q+" and power="+pow);
Assert.assertTrue(MathUtils.compareDoubles(pow,0.7356,1e-4) == 0);
// TEST 2
error = 0.00512;
q = QualityUtils.probToQual(1-error);
double err2 = QualityUtils.qualToErrorProb(q);
pow = w.theoreticalPower(40,q,12,3);
System.out.println("Qual for "+error+"="+q+" back to error="+err2+" and power="+pow);
Assert.assertTrue(MathUtils.compareDoubles(pow,0.2173,1e-4) == 0);
}*/
}