easy-cluster cov-mode 5 doesn't work

[shiraz-shah]

This one should be easy to fix, Martin!

Expected Behavior

Help says:

--cov-mode INT 0: coverage of query and target
                                 ...
               5: short seq. needs to be at least x% of the other seq. length [5]

Current Behavior

mmseqs easy-cluster all.faa all tmp --cov-mode 5 -c 0.85 --threads 64
exists with error:
Unknown coverage mode 5.

MMseqs Output (for bugs)

...

cluster tmp/10137019871064957114/input tmp/10137019871064957114/clu tmp/10137019871064957114/clu_tmp --max-seqs 20 -c 0.85 --cov-mode 5 --spaced-kmer-mode 1 --threads 64 --alignment-mode 3 -e 0.001 --remove-tmp-files 1 

Set cluster sensitivity to -s 6.000000
Set cluster mode SET COVER
Set cluster iterations to 3
Unknown coverage mode 5.
Error: Search died

Context

Coverage mode 5 is important because it's the only option that ensures that clustered sequences are around same size, which is crucial for determining orthology.

Alternatively if size similarity can be ensured otherwise (as a new option), then this option will be freed up to handle alignment coverage proper. This would also be faster since only similarly sized sequences would be compared.

Your Environment

MMseqs2 version: 12.113e3
Server: 72 thread Intel(R) Xeon(R) CPU E5-2699 v3 @ 2.30GHz
OS: Ubuntu Server 18.04

[milot-mirdita]

I think cc47254 should fix the issue.