NAME

       gt-speck - Checks spec definition compliance in GFF3 input.

SYNOPSIS

       gt speck [options] [GFF3_file ...]

DESCRIPTION

       -specfile [filename]
           file with specification definition (default: undefined)

       -colored [yes|no]
           show colored output (default: yes)

       -provideindex [yes|no]
           provide feature index in specfile namespace (requires O(n) memory for n input
           features) (default: no)

       -sort [yes|no]
           sort input before checking (requires O(n) memory for n input features) (default: no)

       -failhard [yes|no]
           stop processing and report runtime errors instead of recording them in the results
           (default: no)

       -output [string]
           output format choose from: [json, text, html, statsonly, tabular] or give path to
           output driver (default: text)

       -typecheck [string]
           use an ontology given in an OBO file to validate parent-child relationships. If no
           argument is given, the sofa.obo file from the gtdata/obo_files directory is used. If
           an argument is given, it is used as an OBO filename. In the case that such a file does
           not exist .obo is added to the argument and loading the resulting filename from the
           gtdata/obo_files directory is attempted. (default: so)

       -seqfile [filename]
           set the sequence file from which to take the sequences (default: undefined)

       -encseq [filename]
           set the encoded sequence indexname from which to take the sequences (default:
           undefined)

       -seqfiles
           set the sequence files from which to extract the features use -- to terminate the list
           of sequence files

       -matchdesc [yes|no]
           search the sequence descriptions from the input files for the desired sequence IDs (in
           GFF3), reporting the first match (default: no)

       -matchdescstart [yes|no]
           exactly match the sequence descriptions from the input files for the desired sequence
           IDs (in GFF3) from the beginning to the first whitespace (default: no)

       -usedesc [yes|no]
           use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence
           entries. If a description contains a sequence range (e.g., III:1000001..2000000), the
           first part is used as sequence ID (III) and the first range position as offset
           (1000001) (default: no)

       -regionmapping [string]
           set file containing sequence-region to sequence file mapping (default: undefined)

       -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)

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

       -help
           display help and exit

       -version
           display version information and exit

REPORTING BUGS

       Report bugs to https://github.com/genometools/genometools/issues.