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Fixed the intermittent PairHMM unit test failure. 

The issue here is that the OptimizedLikelihoodTestProvider uses the same basic underlying class as the
BasicLikelihoodTestProvider and we were using the BasicTestProvider functionality to pull out tests of
that class; so if the optimized tests were run first we were unintentionally running those same tests
again with the basic ones (but expecting different results).
This commit is contained in:
Eric Banks 2013-02-25 14:58:17 -05:00
parent 7519484a38
commit 396b7e0933
1 changed files with 22 additions and 11 deletions
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33
protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
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@ -82,11 +82,12 @@ public class PairHMMUnitTest extends BaseTest {
//
// --------------------------------------------------------------------------------
private class BasicLikelihoodTestProvider extends TestDataProvider {
private class BasicLikelihoodTestProvider {
final String ref, read;
final byte[] refBasesWithContext, readBasesWithContext;
final int baseQual, insQual, delQual, gcp;
final int expectedQual;
final boolean left, right;
final static String CONTEXT = "ACGTAATGACGATTGCA";
final static String LEFT_FLANK = "GATTTATCATCGAGTCTGC";
final static String RIGHT_FLANK = "CATGGATCGTTATCAGCTATCTCGAGGGATTCACTTAACAGTTTTA";
@ -96,7 +97,6 @@ public class PairHMMUnitTest extends BaseTest {
}
public BasicLikelihoodTestProvider(final String ref, final String read, final int baseQual, final int insQual, final int delQual, final int expectedQual, final int gcp, final boolean left, final boolean right) {
super(BasicLikelihoodTestProvider.class, String.format("ref=%s read=%s b/i/d/c quals = %d/%d/%d/%d l/r flank = %b/%b e[qual]=%d", ref, read, baseQual, insQual, delQual, gcp, left, right, expectedQual));
this.baseQual = baseQual;
this.delQual = delQual;
this.insQual = insQual;
@ -104,11 +104,18 @@ public class PairHMMUnitTest extends BaseTest {
this.read = read;
this.ref = ref;
this.expectedQual = expectedQual;
this.left = left;
this.right = right;
refBasesWithContext = asBytes(ref, left, right);
readBasesWithContext = asBytes(read, false, false);
}
@Override
public String toString() {
return String.format("ref=%s read=%s b/i/d/c quals = %d/%d/%d/%d l/r flank = %b/%b e[qual]=%d", ref, read, baseQual, insQual, delQual, gcp, left, right, expectedQual);
}
public double expectedLogL(final PairHMM hmm) {
return (expectedQual / -10.0) + 0.03 +
hmm.getNPotentialXStartsLikelihoodPenaltyLog10(refBasesWithContext.length, readBasesWithContext.length);
@ -178,6 +185,8 @@ public class PairHMMUnitTest extends BaseTest {
final List<Integer> gcps = EXTENSIVE_TESTING ? Arrays.asList(8, 10, 20) : Arrays.asList(10);
final List<Integer> sizes = EXTENSIVE_TESTING ? Arrays.asList(2,3,4,5,7,8,9,10,20,30,35) : Arrays.asList(2);
final List<Object[]> tests = new ArrayList<Object[]>();
for ( final int baseQual : baseQuals ) {
for ( final int indelQual : indelQuals ) {
for ( final int gcp : gcps ) {
@ -188,7 +197,7 @@ public class PairHMMUnitTest extends BaseTest {
final String ref = new String(new byte[]{refBase});
final String read = new String(new byte[]{readBase});
final int expected = refBase == readBase ? 0 : baseQual;
new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp);
tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp)});
}
}
@ -204,10 +213,10 @@ public class PairHMMUnitTest extends BaseTest {
final String ref = insertionP ? small : big;
final String read = insertionP ? big : small;
new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp);
new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, true, false);
new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, false, true);
new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, true, true);
tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp)});
tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, true, false)});
tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, false, true)});
tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, expected, gcp, true, true)});
}
}
}
@ -215,7 +224,7 @@ public class PairHMMUnitTest extends BaseTest {
}
}
return BasicLikelihoodTestProvider.getTests(BasicLikelihoodTestProvider.class);
return tests.toArray(new Object[][]{});
}
@DataProvider(name = "OptimizedLikelihoodTestProvider")
@ -227,6 +236,8 @@ public class PairHMMUnitTest extends BaseTest {
final List<Integer> gcps = EXTENSIVE_TESTING ? Arrays.asList(10, 20, 30) : Arrays.asList(10);
final List<Integer> sizes = EXTENSIVE_TESTING ? Arrays.asList(3, 20, 50, 90, 160) : Arrays.asList(2);
final List<Object[]> tests = new ArrayList<Object[]>();
for ( final int baseQual : baseQuals ) {
for ( final int indelQual : indelQuals ) {
for ( final int gcp : gcps ) {
@ -243,14 +254,14 @@ public class PairHMMUnitTest extends BaseTest {
for ( final boolean leftFlank : Arrays.asList(true, false) )
for ( final boolean rightFlank : Arrays.asList(true, false) )
new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, -0, gcp, leftFlank, rightFlank);
tests.add(new Object[]{new BasicLikelihoodTestProvider(ref, read, baseQual, indelQual, indelQual, -0, gcp, leftFlank, rightFlank)});
}
}
}
}
}
return BasicLikelihoodTestProvider.getTests(BasicLikelihoodTestProvider.class);
return tests.toArray(new Object[][]{});
}
@Test(enabled = !DEBUG, dataProvider = "BasicLikelihoodTestProvider")
@ -262,7 +273,7 @@ public class PairHMMUnitTest extends BaseTest {
double expectedLogL = cfg.expectedLogL(hmm);
// compare to our theoretical expectation with appropriate tolerance
Assert.assertEquals(actualLogL, expectedLogL, cfg.toleranceFromTheoretical(), "Failed with hmm " + hmm + (hmm instanceof Log10PairHMM ? " (" + ((Log10PairHMM)hmm).isDoingExactLog10Calculations() + ")" : ""));
Assert.assertEquals(actualLogL, expectedLogL, cfg.toleranceFromTheoretical(), "Failed with hmm " + hmm);
// compare to the exact reference implementation with appropriate tolerance
Assert.assertEquals(actualLogL, exactLogL, cfg.getTolerance(hmm), "Failed with hmm " + hmm);
Assert.assertTrue(MathUtils.goodLog10Probability(actualLogL), "Bad log10 likelihood " + actualLogL);