Skip to content

Commit

Permalink
Update MAX_GMER_SIZE
Browse files Browse the repository at this point in the history
  • Loading branch information
GuillaumeHolley authored Feb 21, 2022
1 parent 9379ab7 commit a403dd2
Showing 1 changed file with 2 additions and 0 deletions.
2 changes: 2 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,8 @@ SET(MAX_KMER_SIZE "64" CACHE STRING "MAX_KMER_SIZE")

Actual maximum k-mer size is *MAX_KMER_SIZE-1*, e.g maximum *k* is 63 for *MAX_KMER_SIZE=64*. Increasing *MAX_KMER_SIZE* increases Bifrost memory usage (*k*=31 uses 8 bytes of memory per *k*-mer while *k*=63 uses 16 bytes of memory per *k*-mer).

The maximum size of minimizers (*g*-mers) *MAX_GMER_SIZE* can be adjusted the same way as *MAX_KMER_SIZE*. This is especially useful if you want to use a large *k*-mer size but a small *g*-mer size. By default, *MAX_GMER_SIZE* is equal to *MAX_KMER_SIZE*.

To work with larger *k* when using the Bifrost API, the new value *MAX_KMER_SIZE* must be given to the compiler and linker as explained in Section [API](#api)

## Binary usage:
Expand Down

0 comments on commit a403dd2

Please sign in to comment.