'\" t
.\"     Title: gt-tallymer-search
.\"    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\-SEARCH" "1" "07/22/2020" "GenomeTools 1\&.6\&.1" "GenomeTools Manual"
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.SH "NAME"
gt-tallymer-search \- Search a set of k\-mers in an index constructed by ``gt tallymer mkindex\*(Aq\*(Aq\&.
.SH "SYNOPSIS"
.sp
\fBgt tallymer search\fR [options] \-tyr tallymer\-index \-q queryfile0 [queryfile1\&.\&.] [options]
.SH "DESCRIPTION"
.PP
\fB\-tyr\fR [\fIstring\fR]
.RS 4
specify tallymer\-index (default: undefined)
.RE
.PP
\fB\-q\fR
.RS 4
specify query file names
.RE
.PP
\fB\-strand\fR [\fIstring\fR]
.RS 4
specify the strand to be searched: use f (for forward strand) or p (for reverse complemented strand) or fp (for both); default is f (default: f)
.RE
.PP
\fB\-output\fR
.RS 4
specify output flags (qseqnum, qpos, counts, sequence)
.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>\&.