'\" t
.\"     Title: gt-uniq
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 02/28/2024
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.5
.\"  Language: English
.\"
.TH "GT\-UNIQ" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-uniq \- Filter out repeated feature node graphs in a sorted GFF3 file\&.
.SH "SYNOPSIS"
.sp
\fBgt uniq\fR [option \&...] [GFF3_file]
.SH "DESCRIPTION"
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-o\fR [\fIfilename\fR]
.RS 4
redirect output to specified file (default: undefined)
.RE
.PP
\fB\-gzip\fR [\fIyes|no\fR]
.RS 4
write gzip compressed output file (default: no)
.RE
.PP
\fB\-bzip2\fR [\fIyes|no\fR]
.RS 4
write bzip2 compressed output file (default: no)
.RE
.PP
\fB\-force\fR [\fIyes|no\fR]
.RS 4
force writing to output file (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
.sp
A depth\-first traversal of a feature node graph starts at the top\-level feature node (or pseudo\-node) and explores as far along each branch as possible before backtracking\&. Let\(cqs assume that the feature nodes are stored in a list in the order of their traversal (called the \(lqfeature node list\(rq)\&.
.sp
Two feature node graphs are considered to be repeated if their feature node list (from the depth\-first traversal) have the same length and each feature node pair (from both lists at the same position) is \(lqsimilar\(rq\&.
.sp
Two feature nodes are \(lqsimilar\(rq, if they have the same sequence ID, feature type, range, strand, and phase\&.
.sp
For such a repeated feature node graph the one with the higher score (of the top\-level feature) is kept\&. If only one of the feature node graphs has a defined score, this one is kept\&.
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.