'\" t
.\"     Title: gt-tallymer-mkindex
.\"    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\-MKINDE" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-tallymer-mkindex \- Count and index k\-mers in the given enhanced suffix array for a fixed value of k\&.
.SH "SYNOPSIS"
.sp
\fBgt tallymer mkindex\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\-mersize\fR [\fIvalue\fR]
.RS 4
Specify the mer size\&. (default: 20)
.RE
.PP
\fB\-minocc\fR [\fIvalue\fR]
.RS 4
Specify the minimum occurrence number for the mers to output/index (default: 0)
.RE
.PP
\fB\-maxocc\fR [\fIvalue\fR]
.RS 4
Specify the maximum occurrence number for the mers to output/index (default: 0)
.RE
.PP
\fB\-pl\fR [\fIvalue\fR]
.RS 4
specify prefix length for bucket boundary construction recommendation: use without argument; then a reasonable prefix length is automatically determined (default: 0)
.RE
.PP
\fB\-indexname\fR [\fIstring\fR]
.RS 4
store the mers specified by options \-maxocc and \-minocc in an index (default: undefined)
.RE
.PP
\fB\-counts\fR [\fIyes|no\fR]
.RS 4
store counts of the mers (default: no)
.RE
.PP
\fB\-scan\fR [\fIyes|no\fR]
.RS 4
read enhanced suffix array 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>\&.