.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH SAWRITER "1" "January 2019" "sawriter 5.3.2" "User Commands"
.SH NAME
sawriter \- generate suffix arrays for nucleotide sequences
.SH SYNOPSIS
.B sawriter
saOut fastaIn [fastaIn2 fastaIn3 ...] [\-blt p] [\-larsson] [\-4bit] [\-manmy] [\-kar]
.P
.B sawriter
fastaIn  (writes to fastIn.sa).
.SH OPTIONS
\fB\-blt\fR p      Build a lookup table on prefixes of length 'p'. This speeds
.IP
up lookups considerably (more than the LCP table), but misses matches
less than p when searching.
.TP
\fB\-4bit\fR
Read in (one) fasta file as a compressed sequence file.
.TP
\fB\-larsson\fR
(default)  Uses the method of Larsson and Sadakane to build the array.
.TP
\fB\-mamy\fR
Uses the method of MAnber and MYers to build the array (slower than larsson,
.IP
and produces the same result. This is mainly for double checking
the correctness of larsson).
.TP
\fB\-kark\fR
Use Karkkainen DS3 method for building the suffix array.  This will probably be more
slow than larsson, but takes only an extra N/(sqrt 3) extra space.
.TP
\fB\-mafe\fR
(disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina
.TP
\fB\-welter\fR
Use lightweight (sort of light) suffix array construction.  This is a bit more slow than
normal larsson.
.TP
\fB\-welterweight\fR N use a difference cover of size N for building the suffix array.
Valid values are 7,32,64,111, and 2281.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.