Documentation Syntax

[thomns]

Hello,

I was looking at the --help page to adjust coverage but I got very confused as the flag for coverage is -a, which is also a flag for the mm2_options just above it and it can be interpreted as that the flags underneath the mm2_options belong to it instead of being separate. At least that is how I interpreted it and had a few problems (now fixed).

Alignments:
  -mm2_options =STR   space delimited minimap2 parameters. By default ="-a --end-bonus 5 --eqx -N 50 -p 0.5"
  -a A                designate a feature mapped only if it aligns with coverage ≥A; by default A=0.5
  -s S                designate a feature mapped only if its child features (usually exons/CDS) align with sequence identity ≥S; by default S=0.5
  -d D                distance scaling factor; alignment nodes separated by more than a factor of D in the target genome will not be connected in the
                      graph; by default D=2.0
  -flank F            amount of flanking sequence to align as a fraction [0.0-1.0] of gene length. This can improve gene alignment where gene structure
                      differs between target and reference; by default F=0.0

As a suggestion maybe it would be good to clarify that the following alignment flags are not part of the mm2_options.

Many thanks