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.