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 (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