GenomeTools - manual page for GT-INLINESEQ_ADD(1)

## 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.