Provided by: blasr_5.3+0-1build1_amd64 
NAME
sawriter - generate suffix arrays for nucleotide sequences
SYNOPSIS
sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-4bit] [-larsson|-manmy|-kar|-mafe|-welter]
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.
-welterweight N
use a difference cover of size N for building the suffix array. Valid values are 7,32,64,111, and
2281.
SEE ALSO
blasr(1) loadPulses(1) pls2fasta(1) samFilter(1) samtoh5(1) samtom4(1) sdpMatcher(1) toAfg(1)