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This is kind of two issues in one: deciding on output format (should be json for interoperability) and also how to deal with non-unique headers.
Non-unique FASTA headers (discussed online in places previously) I think should be dealt with by checking that the sequence is not duplicated also. If it is duplicated then that redundant entry can be ignored, if it is a novel sequence then throw an error.
Currently outputting an array of objects. Maybe JSON would be better?
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