Strobealign could exit early, i.e., not compute merge_hits_into_nams_forward_and_reverse(), if nonrepetitive_fraction is higher than the threshold we have since strobealign will anyway have to enter find_nams_rescue()
The only case this would fail is if map_param.rescue_levelis set to 0 (through -R 0). However, I have never used anything other than the default rescue level of 1 and don't know it anyone sets this parameter.
Leaving this here for now. We may make some other changes (related to rescue, seed symmetry, and multi-context) that may render this unnecessary.
Strobealign could exit early, i.e., not compute
merge_hits_into_nams_forward_and_reverse(), ifnonrepetitive_fractionis higher than the threshold we have since strobealign will anyway have to enterfind_nams_rescue()The only case this would fail is if
map_param.rescue_levelis set to 0 (through-R 0). However, I have never used anything other than the default rescue level of 1 and don't know it anyone sets this parameter.Leaving this here for now. We may make some other changes (related to rescue, seed symmetry, and multi-context) that may render this unnecessary.