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Fixing ValidateVariants so that it validates deletion records. Fixing GATKdocs.

This commit is contained in:
Ryan Poplin 2011-09-09 12:57:14 -04:00
parent 6ad8943ca0
commit 91c949db74
2 changed files with 6 additions and 10 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -56,11 +56,6 @@ import java.util.Set;
* A variant set to filter. * A variant set to filter.
* </p> * </p>
* *
* <h2>Output</h2>
* <p>
* A filtered VCF.
* </p>
*
* <h2>Examples</h2> * <h2>Examples</h2>
* <pre> * <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \ * java -Xmx2g -jar GenomeAnalysisTK.jar \

11
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -1085,14 +1085,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
} }
public void validateReferenceBases(Allele reference, Byte paddedRefBase) { public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
// don't validate if we're an insertion or complex event // don't validate if we're a complex event
if ( !reference.isNull() && getReference().length() == 1 && !reference.basesMatch(getReference()) ) { if ( !isComplexIndel() && !reference.isNull() && !reference.basesMatch(getReference()) ) {
throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString())); throw new TribbleException.InternalCodecException(String.format("the REF allele is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
} }
// we also need to validate the padding base for simple indels // we also need to validate the padding base for simple indels
if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) ) if ( hasReferenceBaseForIndel() && !getReferenceBaseForIndel().equals(paddedRefBase) ) {
throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, %s vs. %s", getChr(), getStart(), (char)getReferenceBaseForIndel().byteValue(), (char)paddedRefBase.byteValue())); throw new TribbleException.InternalCodecException(String.format("the padded REF base is incorrect for the record at position %s:%d, fasta says %s vs. VCF says %s", getChr(), getStart(), (char)paddedRefBase.byteValue(), (char)getReferenceBaseForIndel().byteValue()));
}
} }
public void validateRSIDs(Set<String> rsIDs) { public void validateRSIDs(Set<String> rsIDs) {