Pufferfish index `--decoys <decoy_list>` option doesn't tell you how to provide a list of FASTA files

[hermidalc]

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?

[hermidalc]

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

[hermidalc]

A solution provided by @rob-p, since internal parser accepts streams, you can do e.g.:

--decoys <(decoys1.fa decoys2.fa)

[hermidalc]

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.