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Darn, forgot to update unit tests.

This commit is contained in:
Eric Banks 2011-08-03 12:31:08 -04:00
parent 020b2408a8
commit db2e0aaa1a
2 changed files with 14 additions and 14 deletions
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2
public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
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@ -135,7 +135,7 @@ public class VCFWriterUnitTest extends BaseTest {
genotypes.put(name,gt); genotypes.put(name,gt);
} }
return new VariantContext("RANDOM",loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, 0, filters, attributes); return new VariantContext("RANDOM",loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, 0, filters, attributes, (byte)'A');
} }

26
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
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@ -92,45 +92,45 @@ public class VariantContextUnitTest {
// test INDELs // test INDELs
alleles = Arrays.asList(Aref, ATC); alleles = Arrays.asList(Aref, ATC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A); alleles = Arrays.asList(ATCref, A);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(Tref, TA, TC); alleles = Arrays.asList(Tref, TA, TC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A, AC); alleles = Arrays.asList(ATCref, A, AC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC")); alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC"));
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
// test MIXED // test MIXED
alleles = Arrays.asList(TAref, T, TC); alleles = Arrays.asList(TAref, T, TC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(TAref, T, AC); alleles = Arrays.asList(TAref, T, AC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(ACref, ATC, AT); alleles = Arrays.asList(ACref, ATC, AT);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(Aref, T, symbolic); alleles = Arrays.asList(Aref, T, symbolic);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
// test SYMBOLIC // test SYMBOLIC
alleles = Arrays.asList(Tref, symbolic); alleles = Arrays.asList(Tref, symbolic);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles); vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC); Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC);
} }
@ -191,7 +191,7 @@ public class VariantContextUnitTest {
@Test @Test
public void testCreatingDeletionVariantContext() { public void testCreatingDeletionVariantContext() {
List<Allele> alleles = Arrays.asList(ATCref, del); List<Allele> alleles = Arrays.asList(ATCref, del);
VariantContext vc = new VariantContext("test", delLoc, delLocStart, delLocStop, alleles); VariantContext vc = new VariantContext("test", delLoc, delLocStart, delLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getChr(), delLoc); Assert.assertEquals(vc.getChr(), delLoc);
Assert.assertEquals(vc.getStart(), delLocStart); Assert.assertEquals(vc.getStart(), delLocStart);
@ -218,7 +218,7 @@ public class VariantContextUnitTest {
@Test @Test
public void testCreatingInsertionVariantContext() { public void testCreatingInsertionVariantContext() {
List<Allele> alleles = Arrays.asList(delRef, ATC); List<Allele> alleles = Arrays.asList(delRef, ATC);
VariantContext vc = new VariantContext("test", insLoc, insLocStart, insLocStop, alleles); VariantContext vc = new VariantContext("test", insLoc, insLocStart, insLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getChr(), insLoc); Assert.assertEquals(vc.getChr(), insLoc);
Assert.assertEquals(vc.getStart(), insLocStart); Assert.assertEquals(vc.getStart(), insLocStart);
@ -251,7 +251,7 @@ public class VariantContextUnitTest {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del)); new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del));
} }
@Test (expectedExceptions = IllegalArgumentException.class) @Test (expectedExceptions = IllegalStateException.class)
public void testBadConstructorArgs3() { public void testBadConstructorArgs3() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(del)); new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(del));
} }