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@ChangqingW
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Adds a new -B flag to support multiple (combinatorial) barcodes, each with their own allow-list

-B '????,name:CB,list:barcodes_x.tsv' -x 'ATCG' -B '????,name:CB2,list:barcodes_x.tsv'

@ChangqingW ChangqingW marked this pull request as draft January 16, 2026 10:54
@olliecheng
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At the moment I've been handling this with multiple piped calls to Flexiplex. While this works 'fine', it would be useful to have it built-in. However, it seems to me that the changes needed to implement this would be quite a significant code change with some questions about ergonomics. For instance:

  • What's the best way to input different barcode lists? The -B syntax now conflicts with the original syntax which could be quite confusing for users
  • How should stats be reported to the user in stderr?
  • Pretty extensive test examples will be needed to assess the edge cases here

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2 participants