NAME

       gt-inlineseq_add - Adds inline sequences from external source to GFF3 input.

SYNOPSIS

       gt inlineseq_add [options] [GFF3_file ...]

DESCRIPTION

       -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 https://github.com/genometools/genometools/issues.

GenomeTools 1.6.5                                  03/31/2024                                GT-INLINESEQ_ADD(1)