Return all primers for pick_sequencing_primers task

[shunhuahan]

• I noticed that only one primer would be returned if the task is pick_sequencing_primers, instead of a list of primer candidates, even if I ask primer3 to return multiple primers using PRIMER_NUM_RETURN.

• I checked the source code and the it appears that the one primer return behavior is enforced by using pick_only_best_primer function (which is only used when pick sequencing primers ) . https://github.com/primer3-org/primer3/blob/43c33e474ba4e70567b72486037feca669eee28f/src/libprimer3.cc#L2420

• My question: Is there any specific reason to return only the "best primer" for pick_sequencing_primers task, and is it possible to update primer3 so that returning multiple primer candidates is an option (e.p. using pick_primer_range function)?

Thanks!

[untergasser]

The pick_sequencing_primers function picks a single primer per position, the best. The user does not have to sort primers afterwards an can just order. If you are interested to obtain several primers, you could create primer lists of that region and sort them by yourself.

Best,

Andreas