The structure of amp_seq_fasta file

[wook2013]

I have read #4 and the example amp_seq_fasta file in the issue. I have a problem that what if I have different sequences between the forward primer and reverse primer with different barcodes?
My data would be like this:

barcode1 forwardprimer amp_seq1 reverseprimer barcode1
barcode2 forwardprimer amp_seq1 reverseprimer barcode2
...
barcode1 forwardprimer amp_seq2 reverseprimer barcode1
barcode2 forwardprimer amp_seq2 reverseprimer barcode2
...

only forwardprimer and reverseprimer are the same but sequence part between them are quite different and may have thousands of possibilities.
if amp_seq is not specified, there should be a way to distinguish and extract forwardprimer and reverseprimer. But I did not find it in the code.

[fangli80]

Please clone the latest version and use --anchor_seq_len to specify your primer length (e.g. --anchor_seq_len 20).

You can use a few Ns to denote the amplicon sequence. For example:

amp_seq.fasta.gz (please unzip before use)

In theory this should work, but I have not tested it on real data because I don't have it. Please let me know if there are any issues.

Thanks,
Li