The main thing we want to prevent is running something for multiple hours, and then failing due to the input being malformed. If possible, it's ideal to shift these checks to early on in a command, to limit user frustration.
The main problem with this right now is the check that the GFA contigs equal the FASTA contigs, done in the partially-mapped read filter in align. Should move that to be earlier.
The main thing we want to prevent is running something for multiple hours, and then failing due to the input being malformed. If possible, it's ideal to shift these checks to early on in a command, to limit user frustration.
The main problem with this right now is the check that the GFA contigs equal the FASTA contigs, done in the partially-mapped read filter in
align. Should move that to be earlier.