See https://github.com/lh3/minimap2 -- asm20 (what we currently use) is the best option for HiFi reads in earlier versions of minimap2 (v2.18 or earlier), but map-hifi should be used for later versions (v2.19 or later).
... It seems like the parameters adjusted based on these settings are slightly different. However, if we use map-hifi, this would instantly fix the minimum minimap2 version to 2.19, and I'm not sure that is worth it.
A solution to this minor dilemma: detect the minimap2 version, and then see if we can use map-hifi; if not, use asm20 (and mention this in the logging output).
See https://github.com/lh3/minimap2 --
asm20(what we currently use) is the best option for HiFi reads in earlier versions of minimap2 (v2.18 or earlier), butmap-hifishould be used for later versions (v2.19 or later).From looking at the code:
https://github.com/lh3/minimap2/blob/e25aa5ee74dda69031ac53d8aca192e4e050164e/options.c#L108-L130
... It seems like the parameters adjusted based on these settings are slightly different. However, if we use
map-hifi, this would instantly fix the minimum minimap2 version to 2.19, and I'm not sure that is worth it.A solution to this minor dilemma: detect the minimap2 version, and then see if we can use
map-hifi; if not, useasm20(and mention this in the logging output).