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Adding matching for deletions that have longer representations #89

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Adding matching for deletions that have longer representations #89

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d529075
Added matching for deletions that have longer representations
calledit Jun 18, 2024
37d1ad7
improved comment explanation
calledit Jun 19, 2024
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8 changes: 8 additions & 0 deletions src/main/java/org/snpsift/annotate/AnnotateVcfDb.java
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Original file line number Diff line number Diff line change
Expand Up @@ -372,6 +372,14 @@ protected boolean match(Variant var, VariantVcfEntry dbEntry) {
if (var.getReference().equalsIgnoreCase(dbEntry.getReference()) //
&& var.getAlt().equalsIgnoreCase(dbEntry.getAlt()) //
) return true;
// check if the db is represeting the same variant using a longer Ref
// (can be the case when the db is not normalized or if the db contains multiple alleles and some of them are longer)
if (dbEntry.getReference().length() > var.getReference().length()) {
String extraRefStr = dbEntry.getReference().substring(var.getReference().length(), dbEntry.getReference().length());
if (var.getReference().concat(extraRefStr).equalsIgnoreCase(dbEntry.getReference()) //
&& var.getAlt().concat(extraRefStr).equalsIgnoreCase(dbEntry.getAlt()) //
) return true;
}
} else {
// No need to use Ref & Alt, it's a match
return true;
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