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assertBiAllelic -> assertMultiAllelic. 

Chris, if this breaks an integration test, you get it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-20 00:09:46 +00:00
parent 2a26bb42dd
commit 761a730758
1 changed files with 6 additions and 5 deletions
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11
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
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@ -77,8 +77,9 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return vcf; return vcf;
} }
public void assertBiAllelic() { public void assertMultiAllelic() {
if (!this.isBiallelic()) throw new StingException("We're not bi-allelic."); if (this.getAlternateBaseList().size() < 1)
throw new StingException("We're not multi-allelic.");
} }
/** /**
@ -120,7 +121,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override @Override
public boolean isSNP() { public boolean isSNP() {
this.assertNotNull(); this.assertNotNull();
assertBiAllelic(); assertMultiAllelic();
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) { for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
if (alt.getType() != VCFGenotypeEncoding.TYPE.SINGLE_BASE) if (alt.getType() != VCFGenotypeEncoding.TYPE.SINGLE_BASE)
return false; return false;
@ -136,7 +137,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override @Override
public boolean isInsertion() { public boolean isInsertion() {
this.assertNotNull(); this.assertNotNull();
assertBiAllelic(); assertMultiAllelic();
if (!mCurrentRecord.hasAlternateAllele()) if (!mCurrentRecord.hasAlternateAllele())
return false; return false;
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) { for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
@ -154,7 +155,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override @Override
public boolean isDeletion() { public boolean isDeletion() {
this.assertNotNull(); this.assertNotNull();
assertBiAllelic(); assertMultiAllelic();
if (!mCurrentRecord.hasAlternateAllele()) if (!mCurrentRecord.hasAlternateAllele())
return false; return false;
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) { for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {