If multiple metadata lines (other than info, format, or filter) have the same key, only one of them is stored. Example: ##contig lines in test/gatk.vcf
This is because they are stored in a dict.
Python doesn't have an associative array without a unique constraint so I'm not sure what the best way around this would be.
The spec is pretty crap on this point. I think we put all of these data in a list.
ie. metadata[key] : [values]
store multiple metadata values with the same key, closes #52