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 https://github.com/genometools/genometools/issues.