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Bugfix for pError not being checked correctly in CommonInfo 

-- UnitTests to ensure correct behavior
-- UnitTests to ensure correct behavior for pass filters vs. failed filters vs. unfiltered
This commit is contained in:
Mark DePristo 2011-11-19 15:58:59 -05:00
parent b7b57ef39a
commit 8f7eebbaaf
3 changed files with 95 additions and 81 deletions
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9
public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java
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@ -107,9 +107,12 @@ final class CommonInfo {
public double getPhredScaledQual() { return getLog10PError() * -10; }
public void setLog10PError(double log10PError) {
if ( this.log10PError > 0 && this.log10PError != NO_LOG10_PERROR) throw new IllegalArgumentException("BUG: log10PError cannot be > 0 : " + this.log10PError);
if ( Double.isInfinite(this.log10PError) ) throw new IllegalArgumentException("BUG: log10PError should not be Infinity");
if ( Double.isNaN(this.log10PError) ) throw new IllegalArgumentException("BUG: log10PError should not be NaN");
if ( log10PError > 0 && log10PError != NO_LOG10_PERROR)
throw new IllegalArgumentException("BUG: log10PError cannot be > 0 : " + this.log10PError);
if ( Double.isInfinite(this.log10PError) )
throw new IllegalArgumentException("BUG: log10PError should not be Infinity");
if ( Double.isNaN(this.log10PError) )
throw new IllegalArgumentException("BUG: log10PError should not be NaN");
this.log10PError = log10PError;
}

75
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
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@ -264,7 +264,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test
public void testCreatingPartiallyCalledGenotype() {
List<Allele> alleles = Arrays.asList(Aref, C);
Genotype g = new Genotype("foo", Arrays.asList(C, Allele.NO_CALL), 10);
Genotype g = new Genotype("foo", Arrays.asList(C, Allele.NO_CALL));
VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(g).make();
Assert.assertTrue(vc.isSNP());
@ -330,13 +330,18 @@ public class VariantContextUnitTest extends BaseTest {
new VariantContextBuilder("test", delLoc, delLocStart, delLocStop, Arrays.asList(Aref, T)).id("").make();
}
@Test (expectedExceptions = Throwable.class)
public void testBadPError() {
new VariantContextBuilder("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref)).log10PError(0.5).make();
}
@Test
public void testAccessingSimpleSNPGenotypes() {
List<Allele> alleles = Arrays.asList(Aref, T);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T));
Genotype g3 = new Genotype("TT", Arrays.asList(T, T));
VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles)
.genotypes(g1, g2, g3).make();
@ -371,12 +376,12 @@ public class VariantContextUnitTest extends BaseTest {
public void testAccessingCompleteGenotypes() {
List<Allele> alleles = Arrays.asList(Aref, T, del);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g4 = new Genotype("Td", Arrays.asList(T, del), 10);
Genotype g5 = new Genotype("dd", Arrays.asList(del, del), 10);
Genotype g6 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T));
Genotype g3 = new Genotype("TT", Arrays.asList(T, T));
Genotype g4 = new Genotype("Td", Arrays.asList(T, del));
Genotype g5 = new Genotype("dd", Arrays.asList(del, del));
Genotype g6 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL));
VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles)
.genotypes(g1, g2, g3, g4, g5, g6).make();
@ -401,9 +406,9 @@ public class VariantContextUnitTest extends BaseTest {
List<Allele> alleles2 = Arrays.asList(Aref);
List<Allele> alleles3 = Arrays.asList(Aref, T, del);
for ( List<Allele> alleles : Arrays.asList(alleles1, alleles2, alleles3)) {
Genotype g1 = new Genotype("AA1", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AA2", Arrays.asList(Aref, Aref), 10);
Genotype g3 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
Genotype g1 = new Genotype("AA1", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AA2", Arrays.asList(Aref, Aref));
Genotype g3 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL));
VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles)
.genotypes(g1, g2, g3).make();
@ -422,20 +427,24 @@ public class VariantContextUnitTest extends BaseTest {
@Test
public void testFilters() {
List<Allele> alleles = Arrays.asList(Aref, T, del);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T));
VariantContext vc = new VariantContextBuilder("test", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(g1, g2).make();
Assert.assertTrue(vc.isNotFiltered());
Assert.assertFalse(vc.isFiltered());
Assert.assertEquals(0, vc.getFilters().size());
Assert.assertFalse(vc.filtersWereApplied());
Assert.assertNull(vc.getFiltersMaybeNull());
vc = new VariantContextBuilder(vc).filters("BAD_SNP_BAD!").make();
Assert.assertFalse(vc.isNotFiltered());
Assert.assertTrue(vc.isFiltered());
Assert.assertEquals(1, vc.getFilters().size());
Assert.assertTrue(vc.filtersWereApplied());
Assert.assertNotNull(vc.getFiltersMaybeNull());
Set<String> filters = new HashSet<String>(Arrays.asList("BAD_SNP_BAD!", "REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE"));
vc = new VariantContextBuilder(vc).filters(filters).make();
@ -443,16 +452,18 @@ public class VariantContextUnitTest extends BaseTest {
Assert.assertFalse(vc.isNotFiltered());
Assert.assertTrue(vc.isFiltered());
Assert.assertEquals(3, vc.getFilters().size());
Assert.assertTrue(vc.filtersWereApplied());
Assert.assertNotNull(vc.getFiltersMaybeNull());
}
@Test
public void testVCFfromGenotypes() {
List<Allele> alleles = Arrays.asList(Aref, T, del);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g4 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T));
Genotype g3 = new Genotype("TT", Arrays.asList(T, T));
Genotype g4 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL));
Genotype g5 = new Genotype("--", Arrays.asList(del, del));
VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, alleles).genotypes(g1,g2,g3,g4,g5).make();
VariantContext vc12 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g2.getSampleName())));
@ -503,9 +514,9 @@ public class VariantContextUnitTest extends BaseTest {
}
public void testGetGenotypeMethods() {
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T));
Genotype g3 = new Genotype("TT", Arrays.asList(T, T));
GenotypesContext gc = GenotypesContext.create(g1, g2, g3);
VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T)).genotypes(gc).make();
@ -608,9 +619,9 @@ public class VariantContextUnitTest extends BaseTest {
@DataProvider(name = "SitesAndGenotypesVC")
public Object[][] MakeSitesAndGenotypesVCs() {
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T));
Genotype g3 = new Genotype("TT", Arrays.asList(T, T));
VariantContext sites = new VariantContextBuilder("sites", snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T)).make();
VariantContext genotypes = new VariantContextBuilder(sites).source("genotypes").genotypes(g1, g2, g3).make();
@ -647,9 +658,9 @@ public class VariantContextUnitTest extends BaseTest {
modified = new VariantContextBuilder(modified).attributes(null).make();
Assert.assertTrue(modified.getAttributes().isEmpty());
Genotype g1 = new Genotype("AA2", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT2", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT2", Arrays.asList(T, T), 10);
Genotype g1 = new Genotype("AA2", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT2", Arrays.asList(Aref, T));
Genotype g3 = new Genotype("TT2", Arrays.asList(T, T));
GenotypesContext gc = GenotypesContext.create(g1,g2,g3);
modified = new VariantContextBuilder(cfg.vc).genotypes(gc).make();
Assert.assertEquals(modified.getGenotypes(), gc);
@ -704,9 +715,9 @@ public class VariantContextUnitTest extends BaseTest {
@Test(dataProvider = "SubContextTest")
public void runSubContextTest(SubContextTest cfg) {
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref));
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T));
Genotype g3 = new Genotype("TT", Arrays.asList(T, T));
GenotypesContext gc = GenotypesContext.create(g1, g2, g3);
VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, Arrays.asList(Aref, T)).genotypes(gc).make();

92
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
View File

@ -409,44 +409,44 @@ public class VariantContextUtilsUnitTest extends BaseTest {
@DataProvider(name = "mergeGenotypes")
public Object[][] mergeGenotypesData() {
new MergeGenotypesTest("TakeGenotypeByPriority-1,2", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)));
new MergeGenotypesTest("TakeGenotypeByPriority-1,2-nocall", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, -1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, -1)));
new MergeGenotypesTest("TakeGenotypeByPriority-2,1", "2,1",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2)));
new MergeGenotypesTest("NonOverlappingGenotypes", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, 2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1), makeG("s2", Aref, T, 2)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, -2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1), makeG("s2", Aref, T, -2)));
new MergeGenotypesTest("PreserveNoCall", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, 2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, 1), makeG("s2", Aref, T, 2)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, -1)),
makeVC("2", Arrays.asList(Aref, T), makeG("s2", Aref, T, -2)),
makeVC("3", Arrays.asList(Aref, T), makeG("s1", Allele.NO_CALL, Allele.NO_CALL, -1), makeG("s2", Aref, T, -2)));
new MergeGenotypesTest("PerserveAlleles", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
makeVC("2", Arrays.asList(Aref, C), makeG("s2", Aref, C, 2)),
makeVC("3", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, 1), makeG("s2", Aref, C, 2)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)),
makeVC("2", Arrays.asList(Aref, C), makeG("s2", Aref, C, -2)),
makeVC("3", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, -1), makeG("s2", Aref, C, -2)));
new MergeGenotypesTest("TakeGenotypePartialOverlap-1,2", "1,2",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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, 1), makeG("s3", Aref, T, 3)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)),
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, -1), makeG("s3", Aref, T, -3)));
new MergeGenotypesTest("TakeGenotypePartialOverlap-2,1", "2,1",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1)),
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("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1)),
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)));
//
// merging genothpes with PLs
@ -454,41 +454,41 @@ public class VariantContextUtilsUnitTest extends BaseTest {
// first, do no harm
new MergeGenotypesTest("OrderedPLs", "1",
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1, 1, 2, 3)),
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1, 1, 2, 3)));
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1, 1, 2, 3)),
makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1, 1, 2, 3)));
// first, do no harm
new MergeGenotypesTest("OrderedPLs-3Alleles", "1",
makeVC("1", Arrays.asList(Aref, C, T), makeG("s1", Aref, T, 1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, C, T), makeG("s1", Aref, T, 1, 1, 2, 3, 4, 5, 6)));
makeVC("1", Arrays.asList(Aref, C, T), makeG("s1", Aref, T, -1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, C, T), makeG("s1", Aref, T, -1, 1, 2, 3, 4, 5, 6)));
// first, do no harm
new MergeGenotypesTest("OrderedPLs-3Alleles-2", "1",
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, 1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, 1, 1, 2, 3, 4, 5, 6)));
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, -1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, -1, 1, 2, 3, 4, 5, 6)));
// first, do no harm
new MergeGenotypesTest("OrderedPLs-3Alleles-2", "1",
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, 1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, T, C), makeG("s2", Aref, C, 1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, 1, 1, 2, 3, 4, 5, 6), makeG("s2", Aref, C, 1, 1, 2, 3, 4, 5, 6)));
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, -1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, T, C), makeG("s2", Aref, C, -1, 1, 2, 3, 4, 5, 6)),
makeVC("1", Arrays.asList(Aref, T, C), makeG("s1", Aref, T, -1, 1, 2, 3, 4, 5, 6), makeG("s2", Aref, C, -1, 1, 2, 3, 4, 5, 6)));
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)));
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)),
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)));
makeVC("3", Arrays.asList(Aref, ATC, T), makeG("s1", Aref, ATC, -1), makeG("s3", Aref, T, -3)));
new MergeGenotypesTest("MultipleSamplePLsDifferentOrder", "1,2",
makeVC("1", Arrays.asList(Aref, C, T), makeG("s1", Aref, C, 1, 1, 2, 3, 4, 5, 6)),
makeVC("2", Arrays.asList(Aref, T, C), makeG("s2", Aref, T, 2, 6, 5, 4, 3, 2, 1)),
makeVC("1", Arrays.asList(Aref, C, T), makeG("s1", Aref, C, -1, 1, 2, 3, 4, 5, 6)),
makeVC("2", Arrays.asList(Aref, T, C), makeG("s2", Aref, T, -2, 6, 5, 4, 3, 2, 1)),
// no likelihoods on result since type changes to mixed multiallelic
makeVC("3", Arrays.asList(Aref, C, T), makeG("s1", Aref, C, 1), makeG("s2", Aref, T, 2)));
makeVC("3", Arrays.asList(Aref, C, T), makeG("s1", Aref, C, -1), makeG("s2", Aref, T, -2)));
return MergeGenotypesTest.getTests(MergeGenotypesTest.class);
}
@ -533,8 +533,8 @@ public class VariantContextUtilsUnitTest extends BaseTest {
@Test
public void testMergeGenotypesUniquify() {
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1));
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2));
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1));
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2));
final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
@ -546,8 +546,8 @@ public class VariantContextUtilsUnitTest extends BaseTest {
@Test(expectedExceptions = UserException.class)
public void testMergeGenotypesRequireUnique() {
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, 1));
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, 2));
final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1));
final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2));
final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,