the fm-index construction function should be moved to the --build step, after the generation of PRG and kmers. The function already dumps the fm-index data structure to a file, so it should just be loaded from that file during the --quasimap step. Especially important for human data, where the fm-index construction takes a few hours
ffranr
commented
6 years ago
the fm-index construction function should be moved to the --build step, after the generation of PRG and kmers. The function already dumps the fm-index data structure to a file, so it should just be loaded from that file during the --quasimap step. Especially important for human data, where the fm-index construction takes a few hours