gt-speck1

Usage

Overview

-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