sawriter(1) generate suffix arrays for nucleotide sequences


sawriter saOut  fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-4bit] [-larsson|-manmy|-kar|-mafe|-welter]

sawriter fastaIn (writes to


-blt p
Build a lookup table on prefixes of length p. This speeds up lookups considerably (more than the LCP table), but misses matches less than p when searching.
Read in (one) fasta file as a compressed sequence file.
-larsson (default) Uses the method of Larsson and Sadakane to build the array.
Uses the method of MAnber and MYers to build the array (slower than larsson, and produces the same result. This is mainly for double checking the correctness of larsson).
Use Karkkainen DS3 method for building the suffix array. This will probably be slower than larsson, but takes only an extra N/(sqrt 3) extra space.
(disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina
Use lightweight (sort of light) suffix array construction. This is a bit more slow than normal larsson.
-welterweight N
use a difference cover of size N for building the suffix array. Valid values are 7,32,64,111, and 2281.