.TH SAWRITER "1" "July 2015" "sawriter 3ca7fe8" "User Commands"
.SH NAME
sawriter \- generate suffix arrays for nucleotide sequences
.SH SYNOPSIS
.B sawriter
.I saOut \0fastaIn
.RI [ fastaIn2
.IR fastaIn3 \0...]
.RB [ \-blt
.IR p ]
.RB [ \-4bit ]
.RB [ \-larsson | \-manmy | \-kar | \-mafe | \-welter ]
.P
.B sawriter
.I fastaIn \fR(writes to fastaIn.sa)
.SH OPTIONS
.TP
.BI \-blt \0p
Build a lookup table on prefixes of length \fIp\fR. This speeds
up lookups considerably (more than the LCP table), but misses matches
less than \fIp\fR when searching.
.TP
.B \-4bit
Read in (one) fasta file as a compressed sequence file.
.TP
.B Methods
.RS
.B \-larsson
(default)  Uses the method of Larsson and Sadakane to build the array.
.TP
.B \-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).
.TP
.B \-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.
.TP
.B \-mafe
(disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina
.TP
.B \-welter
Use lightweight (sort of light) suffix array construction.
This is a bit more slow than normal larsson.
.RE
.TP
.BI \-welterweight \0N
use a difference cover of size \fIN\fR for building the suffix array.
Valid values are 7,32,64,111, and 2281.
.SH SEE ALSO
.BR blasr (1)
.BR loadPulses (1)
.BR pls2fasta (1)
.BR samFilter (1)
.BR samtoh5 (1)
.BR samtom4 (1)
.BR sdpMatcher (1)
.BR toAfg (1)