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Moving the random number generator over to using GenomeAnalysisEngine.getRandomGenerator in the logless versus exact pair hmm unit test. We don't believe this will fix the problem with the non-deterministic test failures but it will give us more information the next time it fails.

This commit is contained in:
Ryan Poplin 2013-02-05 12:44:59 -05:00
parent f6bc5be6b4
commit cb2dd470b6
1 changed files with 5 additions and 5 deletions
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10
protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
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@ -50,6 +50,7 @@ package org.broadinstitute.sting.utils.pairhmm;
// the imports for unit testing. // the imports for unit testing.
import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.Utils;
import org.testng.Assert; import org.testng.Assert;
@ -197,11 +198,10 @@ public class PairHMMUnitTest extends BaseTest {
return BasicLikelihoodTestProvider.getTests(BasicLikelihoodTestProvider.class); return BasicLikelihoodTestProvider.getTests(BasicLikelihoodTestProvider.class);
} }
final Random random = new Random(87860573);
@DataProvider(name = "OptimizedLikelihoodTestProvider") @DataProvider(name = "OptimizedLikelihoodTestProvider")
public Object[][] makeOptimizedLikelihoodTests() { public Object[][] makeOptimizedLikelihoodTests() {
// context on either side is ACGTTGCA REF ACGTTGCA GenomeAnalysisEngine.resetRandomGenerator();
// test all combinations final Random random = GenomeAnalysisEngine.getRandomGenerator();
final List<Integer> baseQuals = EXTENSIVE_TESTING ? Arrays.asList(10, 30, 40, 60) : Arrays.asList(30); final List<Integer> baseQuals = EXTENSIVE_TESTING ? Arrays.asList(10, 30, 40, 60) : Arrays.asList(30);
final List<Integer> indelQuals = EXTENSIVE_TESTING ? Arrays.asList(20, 40, 60) : Arrays.asList(40); final List<Integer> indelQuals = EXTENSIVE_TESTING ? Arrays.asList(20, 40, 60) : Arrays.asList(40);
final List<Integer> gcps = EXTENSIVE_TESTING ? Arrays.asList(10, 20, 30) : Arrays.asList(10); final List<Integer> gcps = EXTENSIVE_TESTING ? Arrays.asList(10, 20, 30) : Arrays.asList(10);
@ -254,8 +254,8 @@ public class PairHMMUnitTest extends BaseTest {
double optimizedLogL = cfg.calcLogL( cachingHMM, false ); double optimizedLogL = cfg.calcLogL( cachingHMM, false );
double loglessLogL = cfg.calcLogL( loglessHMM, false ); double loglessLogL = cfg.calcLogL( loglessHMM, false );
//logger.warn(String.format("Test: logL calc=%.2f optimized=%.2f logless=%.2f expected=%.2f for %s", calculatedLogL, optimizedLogL, loglessLogL, expectedLogL, cfg.toString())); //logger.warn(String.format("Test: logL calc=%.2f optimized=%.2f logless=%.2f expected=%.2f for %s", calculatedLogL, optimizedLogL, loglessLogL, expectedLogL, cfg.toString()));
Assert.assertEquals(optimizedLogL, calculatedLogL, cfg.toleranceFromReference()); Assert.assertEquals(optimizedLogL, calculatedLogL, cfg.toleranceFromReference(), String.format("Test: logL calc=%.2f optimized=%.2f logless=%.2f expected=%.2f for %s", calculatedLogL, optimizedLogL, loglessLogL, exactLogL, cfg.toString()));
Assert.assertEquals(loglessLogL, exactLogL, cfg.toleranceFromExact()); Assert.assertEquals(loglessLogL, exactLogL, cfg.toleranceFromExact(), String.format("Test: logL calc=%.2f optimized=%.2f logless=%.2f expected=%.2f for %s", calculatedLogL, optimizedLogL, loglessLogL, exactLogL, cfg.toString()));
} }
@Test @Test