Alternate allele length of zero

[tfwillems]

When an alternate allele has a length of 0 and there's only 1 alternate allele, the alternate allele field is printed in the VCF as the empty string. While this is technically not incorrect, it causes awk to think there's one less field than every other line in the VCF file. I suspect this will break a lot of subsequent tools, and we may want to consider requiring that alleles have a length >= 1

[mgymrek]

Thanks for point this out. While technically we could have an allele of size 0, I think in almost all such cases it would be a calling error on our part.

Easiest option is to change MIN_ALLELE_SIZE to 1 in ReadContainer.cpp to not allow length 0 alleles.