diff --git a/java/src/org/broadinstitute/sting/playground/utils/PoolUtils.java b/archive/java/src/org/broadinstitute/sting/poolseq/PoolUtils.java similarity index 100% rename from java/src/org/broadinstitute/sting/playground/utils/PoolUtils.java rename to archive/java/src/org/broadinstitute/sting/poolseq/PoolUtils.java diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerUnitTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerUnitTest.java deleted file mode 100644 index f3adb6912..000000000 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerUnitTest.java +++ /dev/null @@ -1,75 +0,0 @@ -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); - - }*/ -}