NAME

       gt-uniq - Filter out repeated feature node graphs in a sorted GFF3 file.

SYNOPSIS

       gt uniq [option ...] [GFF3_file]

DESCRIPTION

       -v [yes|no]
           be verbose (default: no)

       -o [filename]
           redirect output to specified file (default: undefined)

       -gzip [yes|no]
           write gzip compressed output file (default: no)

       -bzip2 [yes|no]
           write bzip2 compressed output file (default: no)

       -force [yes|no]
           force writing to output file (default: no)

       -help
           display help and exit

       -version
           display version information and exit

       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’s
       assume that the feature nodes are stored in a list in the order of their traversal (called
       the “feature node list”).

       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 “similar”.

       Two feature nodes are “similar”, if they have the same sequence ID, feature type, range,
       strand, and phase.

       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.

REPORTING BUGS

       Report bugs to <gt-users@genometools.org>.