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Bug fix: when extracting reference sequence for the event from the reference genome, the tool was treating Deletions and MNPs of length N in exactly the same way: ref_bases[current_pos+1,...,current_pos+N]. This is correct for Deletions but not for MNPs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5258 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2011-02-17 16:15:42 +00:00
parent 497e9ab83b
commit 0e04e95245
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -120,10 +120,14 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
return; return;
} }
// deletions are associated with the (position of) the last (preceding) non-deleted base;
// hence to get actually deleted bases we need offset = 1
int offset = 1 ;
if ( vc.getType() == VariantContext.Type.MNP ) offset = 0; // if it's an MNP, the reported position IS the first modified base
byte[] refBytes = ref.getBases(); byte[] refBytes = ref.getBases();
byte[] trueRef = new byte[reportedRefAllele.length()]; byte[] trueRef = new byte[reportedRefAllele.length()];
for (int i = 0; i < reportedRefAllele.length(); i++) for (int i = 0; i < reportedRefAllele.length(); i++)
trueRef[i] = refBytes[i+1]; trueRef[i] = refBytes[i+offset];
observedRefAllele = Allele.create(trueRef, true); observedRefAllele = Allele.create(trueRef, true);
} }
// SNPs, etc. // SNPs, etc.