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Allowing ./X genotypes and adding a unit test to ensure that this case is covered from now on (especially given that we may want to revert in the future). Reverting this change is really easy and entails uncommenting a few lines of code. But for now, despite Mark's objections, this case is allowed in the VCF spec and we are wrong not to allow it.

This commit is contained in:
Eric Banks 2011-10-19 11:52:05 -04:00
parent 48c4a8cb33
commit 5a6468c11e
2 changed files with 23 additions and 4 deletions
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10
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
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@ -197,14 +197,16 @@ public class Genotype {
if ( alleles == null ) return;
if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0");
int nNoCalls = 0;
// int nNoCalls = 0;
for ( Allele allele : alleles ) {
if ( allele == null )
throw new IllegalArgumentException("BUG: allele cannot be null in Genotype");
nNoCalls += allele.isNoCall() ? 1 : 0;
// nNoCalls += allele.isNoCall() ? 1 : 0;
}
if ( nNoCalls > 0 && nNoCalls != alleles.size() )
throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
// Technically, the spec does allow for the below case so this is not an illegal state
//if ( nNoCalls > 0 && nNoCalls != alleles.size() )
// throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
}
public String getGenotypeString() {

17
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
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@ -252,6 +252,23 @@ public class VariantContextUnitTest extends BaseTest {
Assert.assertEquals(vc.getSampleNames().size(), 0);
}
@Test
public void testCreatingPartiallyCalledGenotype() {
List<Allele> alleles = Arrays.asList(Aref, C);
Genotype g = new Genotype("foo", Arrays.asList(C, Allele.NO_CALL), 10);
VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, alleles, Arrays.asList(g));
Assert.assertTrue(vc.isSNP());
Assert.assertEquals(vc.getNAlleles(), 2);
Assert.assertTrue(vc.hasGenotypes());
Assert.assertFalse(vc.isMonomorphic());
Assert.assertTrue(vc.isPolymorphic());
Assert.assertEquals(vc.getGenotype("foo"), g);
Assert.assertEquals(vc.getChromosomeCount(), 2); // we know that there are 2 chromosomes, even though one isn't called
Assert.assertEquals(vc.getChromosomeCount(Aref), 0);
Assert.assertEquals(vc.getChromosomeCount(C), 1);
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgs1() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref));