Hi Daniel,

For your patch, "<ABC" would be considered a symbolic allele.  I.e. there is a boolean OR operator between the test for "<" and for ">".  Is that really what you intend?

-Alec

On May 20, 2014, at 10:51 PM, Daniel Cameron <notifications@github.com> wrote:

> In src/java/htsjdk/variant/variantcontext/Allele.java:
> 
> >              return false;
> >          else {
> >              final String strBases = new String(bases);
> > -            return (bases[0] == '<' && bases[bases.length-1] == '>') ||
> > -                    (strBases.contains("[") || strBases.contains("]"));
> > +            return (bases[0] == '<' || bases[bases.length-1] == '>') || // symbolic
> 4.2 allows symbolic insertion alleles such as "A" and "A", hence the relaxation of the the <> requirements. < is still rejected as it is <= length 1 (3 lines up), and the VCF specifications do not require a non-zero length ID string, so yes, <> is technically valid (although I don't think it should be).
> 
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