SYNOPSIS
sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [blt p] [4bit] [larssonmanmykarmafewelter]sawriter fastaIn (writes to fastaIn.sa)
OPTIONS
 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.
 4bit
 Read in (one) fasta file as a compressed sequence file.
 Methods


larsson
(default) Uses the method of Larsson and Sadakane to build the array.
 mamy
 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).
 kark
 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.
 mafe
 (disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina
 welter
 Use lightweight (sort of light) suffix array construction. This is a bit more slow than normal larsson.

larsson
(default) Uses the method of Larsson and Sadakane to build the array.
 welterweight N
 use a difference cover of size N for building the suffix array. Valid values are 7,32,64,111, and 2281.