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Reverting previous change. 

Aaron, it's all yours...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1881 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-20 00:55:24 +00:00
parent d21b582b18
commit c29924e7cf
1 changed files with 5 additions and 6 deletions
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11
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
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@ -77,9 +77,8 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
return vcf; return vcf;
} }
public void assertMultiAllelic() { public void assertBiAllelic() {
if (this.getAlternateBaseList().size() < 1) if (!this.isBiallelic()) throw new StingException("We're not bi-allelic.");
throw new StingException("We're not multi-allelic.");
} }
/** /**
@ -121,7 +120,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override @Override
public boolean isSNP() { public boolean isSNP() {
this.assertNotNull(); this.assertNotNull();
assertMultiAllelic(); assertBiAllelic();
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;
@ -137,7 +136,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override @Override
public boolean isInsertion() { public boolean isInsertion() {
this.assertNotNull(); this.assertNotNull();
assertMultiAllelic(); assertBiAllelic();
if (!mCurrentRecord.hasAlternateAllele()) if (!mCurrentRecord.hasAlternateAllele())
return false; return false;
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) { for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
@ -155,7 +154,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
@Override @Override
public boolean isDeletion() { public boolean isDeletion() {
this.assertNotNull(); this.assertNotNull();
assertMultiAllelic(); assertBiAllelic();
if (!mCurrentRecord.hasAlternateAllele()) if (!mCurrentRecord.hasAlternateAllele())
return false; return false;
for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) { for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {