'\" t
.\"     Title: gt-speck
.\"    Author: [FIXME: author] [see http://www.docbook.org/tdg5/en/html/author]
.\" Generator: DocBook XSL Stylesheets vsnapshot <http://docbook.sf.net/>
.\"      Date: 02/28/2024
.\"    Manual: GenomeTools Manual
.\"    Source: GenomeTools 1.6.5
.\"  Language: English
.\"
.TH "GT\-SPECK" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-speck \- Checks spec definition compliance in GFF3 input\&.
.SH "SYNOPSIS"
.sp
\fBgt speck\fR [options] [GFF3_file \&...]
.SH "DESCRIPTION"
.PP
\fB\-specfile\fR [\fIfilename\fR]
.RS 4
file with specification definition (default: undefined)
.RE
.PP
\fB\-colored\fR [\fIyes|no\fR]
.RS 4
show colored output (default: yes)
.RE
.PP
\fB\-provideindex\fR [\fIyes|no\fR]
.RS 4
provide feature index in specfile namespace (requires O(n) memory for n input features) (default: no)
.RE
.PP
\fB\-sort\fR [\fIyes|no\fR]
.RS 4
sort input before checking (requires O(n) memory for n input features) (default: no)
.RE
.PP
\fB\-failhard\fR [\fIyes|no\fR]
.RS 4
stop processing and report runtime errors instead of recording them in the results (default: no)
.RE
.PP
\fB\-output\fR [\fIstring\fR]
.RS 4
output format choose from: [json, text, html, statsonly, tabular] or give path to output driver (default: text)
.RE
.PP
\fB\-typecheck\fR [\fIstring\fR]
.RS 4
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
\fI\&.obo\fR
is added to the argument and loading the resulting filename from the gtdata/obo_files directory is attempted\&. (default: so)
.RE
.PP
\fB\-seqfile\fR [\fIfilename\fR]
.RS 4
set the sequence file from which to take the sequences (default: undefined)
.RE
.PP
\fB\-encseq\fR [\fIfilename\fR]
.RS 4
set the encoded sequence indexname from which to take the sequences (default: undefined)
.RE
.PP
\fB\-seqfiles\fR
.RS 4
set the sequence files from which to extract the features use
\fI\-\-\fR
to terminate the list of sequence files
.RE
.PP
\fB\-matchdesc\fR [\fIyes|no\fR]
.RS 4
search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)
.RE
.PP
\fB\-matchdescstart\fR [\fIyes|no\fR]
.RS 4
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)
.RE
.PP
\fB\-usedesc\fR [\fIyes|no\fR]
.RS 4
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 (\fIIII\fR) and the first range position as offset (\fI1000001\fR) (default: no)
.RE
.PP
\fB\-regionmapping\fR [\fIstring\fR]
.RS 4
set file containing sequence\-region to sequence file mapping (default: undefined)
.RE
.PP
\fB\-o\fR [\fIfilename\fR]
.RS 4
redirect output to specified file (default: undefined)
.RE
.PP
\fB\-gzip\fR [\fIyes|no\fR]
.RS 4
write gzip compressed output file (default: no)
.RE
.PP
\fB\-bzip2\fR [\fIyes|no\fR]
.RS 4
write bzip2 compressed output file (default: no)
.RE
.PP
\fB\-force\fR [\fIyes|no\fR]
.RS 4
force writing to output file (default: no)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.RE
.PP
\fB\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.