Closed hermidalc closed 2 years ago
Seems like option only allows for one decoy FASTA file? The help should be updated to make that clear
https://github.com/COMBINE-lab/pufferfish/blob/develop/src/Pufferfish.cpp#L152
A solution provided by @rob-p, since internal parser accepts streams, you can do e.g.:
--decoys <(decoys1.fa decoys2.fa)
Thanks @rob-p for the clarification that the --decoys
should be a file with the list of the sequence IDs in the reference FASTA passed to --ref
that should be considered decoys.
The
--decoys <decoy_list>
option doesn't tell you how to provide a list of FASTA files. If I do--decoys decoys1.fa decoys2.fa
that doesn't work, if I do--decoys decoys1.fa,decoys2.fa
that also doesn't work. How do you provide a list of decoy FASTA files using this option?