NAME

       gt-chseqids - Change sequence ids by the mapping given in a mapping file.

SYNOPSIS

       gt chseqids [option ...] mapping_file [GFF3_file]

DESCRIPTION

       -sort [yes|no]
           sort the GFF3 features after changing the sequence ids (memory consumption is
           proportional to the input file size) (default: no)

       -v [yes|no]
           be verbose (default: no)

       -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

       File format for mapping_file:

       The supplied mapping file defines a mapping table named “chseqids”. It maps the
       sequence-region entries given in the GFF3_file to other names. It can be defined as
       follows:

           chseqids = {
             chr1  = "seq1",
             chr2  = "seq2"
           }

       When this example is used, all sequence ids “chr1” will be changed to “seq1” and all
       sequence ids “chr2” to “seq2”.

REPORTING BUGS

       Report bugs to https://github.com/genometools/genometools/issues.