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Added unit tests to test genotype merges with PL's

This commit is contained in:
Guillermo del Angel 2011-09-24 21:17:15 -04:00
parent 203517fbb7
commit 4707ab4a7d
1 changed files with 17 additions and 9 deletions
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26
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
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@ -66,6 +66,11 @@ public class VariantContextUtilsUnitTest extends BaseTest {
return new Genotype(sample, Arrays.asList(a1, a2)); return new Genotype(sample, Arrays.asList(a1, a2));
} }
private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError, double l1, double l2, double l3) {
return new Genotype(sample, Arrays.asList(a1, a2), log10pError, new double[]{l1,l2,l3});
}
private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError) { private Genotype makeG(String sample, Allele a1, Allele a2, double log10pError) {
return new Genotype(sample, Arrays.asList(a1, a2), log10pError); return new Genotype(sample, Arrays.asList(a1, a2), log10pError);
} }
@ -189,13 +194,6 @@ public class VariantContextUtilsUnitTest extends BaseTest {
inputs, priority, inputs, priority,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false); VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false);
System.out.println("expected:");
System.out.println(cfg.expected.toString());
System.out.println("inputs");
for (VariantContext vc:inputs)
System.out.println(vc.toString());
System.out.println("merged:");
System.out.println(merged.toString());
Assert.assertEquals(merged.getAlleles(), cfg.expected); Assert.assertEquals(merged.getAlleles(), cfg.expected);
} }
@ -448,7 +446,17 @@ public class VariantContextUtilsUnitTest extends BaseTest {
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)), makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3))); makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2), makeG("s3", Aref, T, 3)));
// todo -- GDA -- add tests for merging correct PLs // merging genothpes with PLs
new MergeGenotypesTest("TakeGenotypePartialOverlapWithPLs-2,1", "2,1",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1,5,0,3)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2,4,0,2), makeG("s3", Aref, T, 3,3,0,2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2,4,0,2), makeG("s3", Aref, T, 3,3,0,2)));
new MergeGenotypesTest("TakeGenotypePartialOverlapWithPLs-1,2", "1,2",
makeVC("1", Arrays.asList(Aref,ATC), makeG("s1", Aref, ATC, 1,5,0,3)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2,4,0,2), makeG("s3", Aref, T, 3,3,0,2)),
// no likelihoods on result since type changes to mixed multiallelic
makeVC("3", Arrays.asList(Aref, ATC, T), makeG("s1", Aref, ATC, 1), makeG("s3", Aref, T, 3)));
return MergeGenotypesTest.getTests(MergeGenotypesTest.class); return MergeGenotypesTest.getTests(MergeGenotypesTest.class);
} }
@ -489,7 +497,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
Assert.assertEquals(value.getNegLog10PError(), expectedValue.getNegLog10PError()); Assert.assertEquals(value.getNegLog10PError(), expectedValue.getNegLog10PError());
Assert.assertEquals(value.hasLikelihoods(), expectedValue.hasLikelihoods()); Assert.assertEquals(value.hasLikelihoods(), expectedValue.hasLikelihoods());
if ( value.hasLikelihoods() ) if ( value.hasLikelihoods() )
Assert.assertEquals(value.getLikelihoods(), expectedValue.getLikelihoods()); Assert.assertEquals(value.getLikelihoods().getAsVector(), expectedValue.getLikelihoods().getAsVector());
} }
} }