In help page of easy-cluster module, default value for -c is 0.000. -c is for alignment (List matches above this fraction of aligned (covered) residues (see --cov-mode) (default: 0.0); higher coverage = more global alignment).
-c FLOAT List matches above this fraction of aligned (covered) residues (see --cov-mode) [0.000]
Current Behavior
But when I run easy-cluster module with default value for -c, the result is not the result with using 0.000 for -c. The value for -c should be about 0.800, which is same with default value for -c in cluster module.
Expected Behavior
In help page of easy-cluster module, default value for -c is 0.000. -c is for alignment (List matches above this fraction of aligned (covered) residues (see --cov-mode) (default: 0.0); higher coverage = more global alignment).
-c FLOAT List matches above this fraction of aligned (covered) residues (see --cov-mode) [0.000]Current Behavior
But when I run easy-cluster module with default value for -c, the result is not the result with using 0.000 for -c. The value for -c should be about 0.800, which is same with default value for -c in cluster module.
Steps to Reproduce (for bugs)
foldseek easy-cluster /folder/to/inputdb /cluster/name tmp -e 1.000E+05 foldseek easy-cluster /folder/to/inputdb /cluster/name tmp -c 0.800 -e 1.000E+05
Foldssek Output (for bugs)
These two code give the same result. But the default value for -c is 0.000.
Context
The default value for -c in easy-cluster module shoud be changed to correct one in help page.
Your Environment
CentOS Linux 7 (Core) foldseek version: 8.ef4e960 from bioconda Also checked in newest version 9.427df8a from bioconda