NAME

       gt-gff3 - Parse, possibly transform, and output GFF3 files.

SYNOPSIS

       gt gff3 [option ...] [GFF3_file ...]

OPTIONS

       -sort
           sort the GFF3 features (memory consumption is proportional to the input file size(s))
           (default: no)

       -tidy
           try to tidy the GFF3 files up during parsing (default: no)

       -retainids
           when available, use the original IDs provided in the source file (memory consumption
           is proportional to the input file size(s)) (default: no)

       -checkids
           make sure the ID attributes are unique within the scope of each GFF3_file, as required
           by GFF3 specification (memory consumption is proportional to the input file size(s))
           (default: no)

       -addids
           add missing "##sequence-region" lines automatically (default: yes)

       -fixregionboundaries
           automatically adjust "##sequence-region" lines to contain all their features (memory
           consumption is proportional to the input file size(s)) (default: no)

       -addintrons
           add intron features between existing exon features (default: no)

       -offset
           transform all features by the given offset (default: undefined)

       -offsetfile
           transform all features by the offsets given in file (default: undefined)

       -typecheck
           check GFF3 types against "id" and "name" tags in given OBO file (default: undefined)

       -show
           show GFF3 output (default: yes)

       -v
           be verbose (default: no)

       -width
           set output width for FASTA sequence printing (0 disables formatting) (default: 0)

       -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

       File format for option -offsetfile:

       The file supplied to option -offsetfile defines a mapping table named “offsets”. It maps
       the sequence-regions given in the GFF3_file to offsets. It can be defined as follows:

       offsets = { chr1 = 1000, chr2 = 500 }

       When this example is used, all features with seqid “chr1” will be offset by 1000 and all
       features with seqid “chr2” by 500.

       If -offsetfile is used, offsets for all sequence-regions contained in the given GFF3 files
       must be defined.

AUTHOR

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

                                            10/07/2012                                 GT-GFF3(1)