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Validate that the reference padding base for indels is correct.

This commit is contained in:
Eric Banks 2011-08-04 12:48:56 -04:00
parent f10588420c
commit e48492f3c3
2 changed files with 10 additions and 5 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -154,10 +154,10 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
try { try {
switch( type ) { switch( type ) {
case ALL: case ALL:
vc.extraStrictValidation(observedRefAllele, rsIDs); vc.extraStrictValidation(observedRefAllele, ref.getBase(), rsIDs);
break; break;
case REF: case REF:
vc.validateReferenceBases(observedRefAllele); vc.validateReferenceBases(observedRefAllele, ref.getBase());
break; break;
case IDS: case IDS:
vc.validateRSIDs(rsIDs); vc.validateRSIDs(rsIDs);

11
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -1055,11 +1055,12 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* Run all extra-strict validation tests on a Variant Context object * Run all extra-strict validation tests on a Variant Context object
* *
* @param reference the true reference allele * @param reference the true reference allele
* @param paddedRefBase the reference base used for padding indels
* @param rsIDs the true dbSNP IDs * @param rsIDs the true dbSNP IDs
*/ */
public void extraStrictValidation(Allele reference, Set<String> rsIDs) { public void extraStrictValidation(Allele reference, Byte paddedRefBase, Set<String> rsIDs) {
// validate the reference // validate the reference
validateReferenceBases(reference); validateReferenceBases(reference, paddedRefBase);
// validate the RS IDs // validate the RS IDs
validateRSIDs(rsIDs); validateRSIDs(rsIDs);
@ -1074,11 +1075,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
//checkReferenceTrack(); //checkReferenceTrack();
} }
public void validateReferenceBases(Allele reference) { public void validateReferenceBases(Allele reference, Byte paddedRefBase) {
// don't validate if we're an insertion // don't validate if we're an insertion
if ( !reference.isNull() && !reference.basesMatch(getReference()) ) { if ( !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, %s vs. %s", getChr(), getStart(), reference.getBaseString(), getReference().getBaseString()));
} }
// we also need to validate the padding base for simple indels
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()));
} }
public void validateRSIDs(Set<String> rsIDs) { public void validateRSIDs(Set<String> rsIDs) {