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Bugfix to ensure the DB=1 old files decode properly

This commit is contained in:
Mark DePristo 2012-06-25 13:14:55 -04:00
parent c1ac0e2760
commit 39c849aced
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -1431,7 +1431,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
switch ( format.getType() ) { switch ( format.getType() ) {
case Character: return string; case Character: return string;
case Flag: case Flag:
final boolean b = Boolean.valueOf(string); final boolean b = Boolean.valueOf(string) || string.equals("1");
if ( b == false ) if ( b == false )
throw new UserException.MalformedVCF("VariantContext FLAG fields " + field + " cannot contain false values" throw new UserException.MalformedVCF("VariantContext FLAG fields " + field + " cannot contain false values"
+ " as seen at " + getChr() + ":" + getStart()); + " as seen at " + getChr() + ":" + getStart());