gts-repair - repair fragmented features
gts-repair [--version] [-h | --help] [args] seqin
gts-repair takes a single input sequence and attempts to reconstruct features that have been fragmented as a result of other manipulations. Specifically, gts-repair will scan each sequence to find features that have identical feature keys and qualifier key-value pairs, check if their locations are pointing to a consecutive region of the sequence, and if they are, merge the locations to create a single feature. Any features that has been lost as a result of other manipulations will not be reconstructed.
<seqin>Input sequence file (may be omitted if standard input is provided). See gts-seqin(7) for a list of currently supported list of sequence formats.
-F <format>, --format=<format>Output file format (defaults to same as input). See gts-seqout(7) for a list of currently supported list of sequence formats. The format specified with this option will override the file type detection from the output filename.
--no-cacheDo not use or create cache. See gts-cache(7) for details.
-o <output>, --output=<output>Output sequence file (specifying - will force standard output). The
output file format will be automatically detected from the filename if none
is specified with the -F or --format option.
gts-repair currently has no known bugs.
gts-repair is written and maintained by Kotone Itaya.
gts(1), gts-join(1), gts-seqin(7), gts-seqout(7)