'\" t
.\"     Title: gt-chseqids
.\"    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\-CHSEQIDS" "1" "02/28/2024" "GenomeTools 1\&.6\&.5" "GenomeTools Manual"
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.SH "NAME"
gt-chseqids \- Change sequence ids by the mapping given in a mapping file\&.
.SH "SYNOPSIS"
.sp
\fBgt chseqids\fR [option \&...] mapping_file [GFF3_file]
.SH "DESCRIPTION"
.PP
\fB\-sort\fR [\fIyes|no\fR]
.RS 4
sort the GFF3 features after changing the sequence ids (memory consumption is proportional to the input file size) (default: no)
.RE
.PP
\fB\-v\fR [\fIyes|no\fR]
.RS 4
be verbose (default: no)
.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\-help\fR
.RS 4
display help and exit
.RE
.PP
\fB\-version\fR
.RS 4
display version information and exit
.RE
.sp
File format for mapping_file:
.sp
The supplied mapping file defines a mapping table named \(lqchseqids\(rq\&. It maps the sequence\-region entries given in the GFF3_file to other names\&. It can be defined as follows:
.sp
.if n \{\
.RS 4
.\}
.nf
chseqids = {
  chr1  = "seq1",
  chr2  = "seq2"
}
.fi
.if n \{\
.RE
.\}
.sp
When this example is used, all sequence ids \(lqchr1\(rq will be changed to \(lqseq1\(rq and all sequence ids \(lqchr2\(rq to \(lqseq2\(rq\&.
.SH "REPORTING BUGS"
.sp
Report bugs to https://github\&.com/genometools/genometools/issues\&.