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Bug fix for VariantsToVCF: old dbSNP files can have '-' as reference base and those records always need to be padded.

This commit is contained in:
Eric Banks 2013-01-16 16:15:58 -05:00
parent 4cf34ee9da
commit 79bc818022
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -194,17 +194,18 @@ public class VariantContextAdaptors {
return null; // we weren't given enough reference context to create the VariantContext return null; // we weren't given enough reference context to create the VariantContext
final byte refBaseForIndel = ref.getBases()[index]; final byte refBaseForIndel = ref.getBases()[index];
final boolean refBaseIsDash = dbsnp.getNCBIRefBase().equals("-");
boolean addPaddingBase; boolean addPaddingBase;
if ( isSNP(dbsnp) || isMNP(dbsnp) ) if ( isSNP(dbsnp) || isMNP(dbsnp) )
addPaddingBase = false; addPaddingBase = false;
else if ( isIndel(dbsnp) || dbsnp.getVariantType().contains("mixed") ) else if ( isIndel(dbsnp) || dbsnp.getVariantType().contains("mixed") )
addPaddingBase = VariantContextUtils.requiresPaddingBase(stripNullDashes(getAlleleList(dbsnp))); addPaddingBase = refBaseIsDash || VariantContextUtils.requiresPaddingBase(stripNullDashes(getAlleleList(dbsnp)));
else else
return null; // can't handle anything else return null; // can't handle anything else
Allele refAllele; Allele refAllele;
if ( dbsnp.getNCBIRefBase().equals("-") ) if ( refBaseIsDash )
refAllele = Allele.create(refBaseForIndel, true); refAllele = Allele.create(refBaseForIndel, true);
else if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) ) else if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
return null; return null;