min-dc-hmm-coverage flag meaning

[nsneeladrisen]

for the cath-resolve-hits command, this flag has no associated function in the help section. Adding it will be helpful!

[tonyelewis]

The reason it isn't documented in the usage message is because it doesn't exist and you never saw it :wave:.

Well… OK… it does exist. But it isn't an official, publicly-supported option; it's a hacky thing we bunged in because it was convenient for our OrengoGroup needs at the time.

If you're in the know, you can run ./cath-resolve-hits --hidden-help and then the usage message includes:

[…]
Hit filtering [hidden options]:
  --min-hmm-coverage [=<percent>(=50)]           [IN PUBLIC GENE3D COMMAND] In hmmsearch_out input, ignore any hits for which 100.0 * ( hmm_to + 1 - hmm_from ) / hmm_length  <  <percent>
  --min-dc-hmm-coverage [=<percent>(=80)]        [IN PUBLIC GENE3D COMMAND] In hmmsearch_out input, ignore any /^\dc_{32}$/ hits for which 100.0 * ( hmm_to + 1 - hmm_from ) / hmm_length  <  <percent>
[…]

I'm open to discussion about how to improve things.