GT-UNIQ(1)

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

SYNOPSIS

gt uniq [option ...] [GFF3_file]

OPTIONS

-v
    be verbose (default: no)

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

-gzip
    write gzip compressed output file (default: no)

-bzip2
    write bzip2 compressed output file (default: no)

-force
    force writing to output file (default: no)

-help
    display help and exit

-version
    display version information and exit

DESCRIPTION

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 lis t (from the depth-first traversal) have the same length and each feature node pai r (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 define d score, this one is kept.

AUTHOR

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