In the ranks branch, gramtools precalculates the ranks array, but doesn't store it to file, so this step is made redundantly when mapping each sample. Should read in from file if the precalculation was already made and as with the kmers, the rank precalc step should be moved from --quasimap to --build and result stored in the cache dir.
ffranr
commented
6 years ago
In the ranks branch, gramtools precalculates the ranks array, but doesn't store it to file, so this step is made redundantly when mapping each sample. Should read in from file if the precalculation was already made and as with the kmers, the rank precalc step should be moved from --quasimap to --build and result stored in the cache dir.