When I added the RED repeatmasker, the intention was to replace the lastz masker by default. This is how cactus works, but cactus-preprocess still runs the lastz masker after Red.
This PR fixes cactus-preprocess to just run Red by default. It also fixes the --maskMode option so that it works as described (runs only the selected masker).
I noticed this while trying to reproduce #1370.
When I added the RED repeatmasker, the intention was to replace the lastz masker by default. This is how
cactusworks, butcactus-preprocessstill runs the lastz masker after Red.This PR fixes
cactus-preprocessto just run Red by default. It also fixes the--maskModeoption so that it works as described (runs only the selected masker).