Bugfix to ensure the DB=1 old files decode properly

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