From cb2dd470b6339ba024783c83a3bb656271f267d0 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 5 Feb 2013 12:44:59 -0500 Subject: [PATCH] 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. --- .../sting/utils/pairhmm/PairHMMUnitTest.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java index 87e208af4..8c09d23b8 100644 --- a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java +++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java @@ -50,6 +50,7 @@ package org.broadinstitute.sting.utils.pairhmm; // the imports for unit testing. import org.broadinstitute.sting.BaseTest; +import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; import org.testng.Assert; @@ -197,11 +198,10 @@ public class PairHMMUnitTest extends BaseTest { return BasicLikelihoodTestProvider.getTests(BasicLikelihoodTestProvider.class); } - final Random random = new Random(87860573); @DataProvider(name = "OptimizedLikelihoodTestProvider") public Object[][] makeOptimizedLikelihoodTests() { - // context on either side is ACGTTGCA REF ACGTTGCA - // test all combinations + GenomeAnalysisEngine.resetRandomGenerator(); + final Random random = GenomeAnalysisEngine.getRandomGenerator(); final List baseQuals = EXTENSIVE_TESTING ? Arrays.asList(10, 30, 40, 60) : Arrays.asList(30); final List indelQuals = EXTENSIVE_TESTING ? Arrays.asList(20, 40, 60) : Arrays.asList(40); final List 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 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())); - Assert.assertEquals(optimizedLogL, calculatedLogL, cfg.toleranceFromReference()); - Assert.assertEquals(loglessLogL, exactLogL, cfg.toleranceFromExact()); + 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(), String.format("Test: logL calc=%.2f optimized=%.2f logless=%.2f expected=%.2f for %s", calculatedLogL, optimizedLogL, loglessLogL, exactLogL, cfg.toString())); } @Test