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.\"     Title: gt-tallymer-occratio
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 07/22/2020
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.1
.\"  Language: English
.\"
.TH "GT\-TALLYMER\-OCCRAT" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-tallymer-occratio \- Compute occurrence ratio for a set of sequences represented by an enhanced suffix array\&.
.SH "SYNOPSIS"
.sp
\fBgt tallymer occratio\fR [options] \-esa suffixerator\-index [options]
.SH "DESCRIPTION"
.PP
\fB\-esa\fR [\fIstring\fR]
.RS 4
specify suffixerator\-index (mandatory option) (default: undefined)
.RE
.PP
\fB\-minmersize\fR [\fIvalue\fR]
.RS 4
specify minimum mer size for which to compute the occurrence distribution (default: 0)
.RE
.PP
\fB\-maxmersize\fR [\fIvalue\fR]
.RS 4
specify maximum mer size for which to compute the occurrence distribution (default: 0)
.RE
.PP
\fB\-step\fR [\fIvalue\fR]
.RS 4
specify step size when specifying mer sizes (default: 1)
.RE
.PP
\fB\-mersizes\fR
.RS 4
specify mer sizes as non\-empty sequence of non decreasing positive integers
.RE
.PP
\fB\-output\fR
.RS 4
use combination of the following keywords: unique nonunique nonuniquemulti relative total to specify kind of output
.RE
.PP
\fB\-scan\fR [\fIyes|no\fR]
.RS 4
read suffixerator\-index sequentially instead of mapping it to 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>\&.