'\" t
.\"     Title: gt-repfind
.\"    Author: [FIXME: author] [see http://docbook.sf.net/el/author]
.\" Generator: DocBook XSL Stylesheets v1.79.1 <http://docbook.sf.net/>
.\"      Date: 01/06/2017
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.5.9
.\"  Language: English
.\"
.TH "GT\-REPFIND" "1" "01/06/2017" "GenomeTools 1\&.5\&.9" "GenomeTools Manual"
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.SH "NAME"
gt-repfind \- Compute maximal exact matches (and more)\&.
.SH "SYNOPSIS"
.sp
\fBgt repfind\fR [options] \-ii indexname
.SH "DESCRIPTION"
.PP
\fB\-l\fR [\fIvalue\fR]
.RS 4
Specify minimum length of matches (default: 0)
.RE
.PP
\fB\-f\fR [\fIyes|no\fR]
.RS 4
Compute forward matches (default: yes)
.RE
.PP
\fB\-r\fR [\fIyes|no\fR]
.RS 4
Compute reverse matches (default: no)
.RE
.PP
\fB\-p\fR [\fIyes|no\fR]
.RS 4
Compute matches on reverse strand (default: no)
.RE
.PP
\fB\-seedlength\fR [\fIvalue\fR]
.RS 4
Specify minimum length of seed (default: 0)
.RE
.PP
\fB\-maxfreq\fR [\fIvalue\fR]
.RS 4
Specify maximal frequency of maximal exact matches in reference sequence (default: 0)
.RE
.PP
\fB\-extendxdrop\fR [\fIvalue\fR]
.RS 4
Extend seed to both sides using xdrop algorithm, optional parameter specifies sensitivity (default: 97)
.RE
.PP
\fB\-xdropbelow\fR [\fIvalue\fR]
.RS 4
Specify xdrop cutoff score (argument 0 means undefined)\&. If undefined an optimal value is determined automatically depending on the error rate
.RE
.PP
\fB\-extendgreedy\fR [\fIvalue\fR]
.RS 4
Extend seed to both sides using greedy algorithm with trimming of waves, optional parameter specifies sensitivity (default: 97)
.RE
.PP
\fB\-minidentity\fR [\fIvalue\fR]
.RS 4
Specify minimum identity of matches as integer in the range from 70 to 99 (for xdrop and greedy extension) (default: 80)
.RE
.PP
\fB\-a\fR [\fIvalue\fR]
.RS 4
show alignments/sequences for exact matches (optional argument is number of columns per line) (default: 70)
.RE
.PP
\fB\-ii\fR [\fIstring\fR]
.RS 4
Specify input index (default: undefined)
.RE
.PP
\fB\-scan\fR [\fIyes|no\fR]
.RS 4
scan index rather than map it to main memory (default: no)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to <kurtz@zbh\&.uni\-hamburg\&.de>\&.