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)
- -v [yes|no]
-
be verbose (default: no)
- -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)
- -help
-
display help and exit
- -version
-
display version information and exit
REPORTING BUGS
Report bugs to <gt-users@genometools.org>.