SYNOPSIS

DESCRIPTION

-d|--debug:

Print debugging messages

-h|--help:

Print help message and exit

-l|--delta: INT

Extend gene loci by this many nucleotides; default is 0

-V|--verbose:

Print verbose warning messages

-v|--version:

Print version number and exit

Output options:

-a|--datashare: STRING

Location from which to copy shared data for HTML output (if `make install' has not yet been run)

-f|--outformat: STRING

Indicate desired output format; possible options: 'csv', 'text', or 'html' (default='text'); in 'text' or 'csv' mode, will create a single file; in 'html' mode, will create a directory

-g|--nogff3:

Do no print GFF3 output corresponding to each comparison

-o|--outfile: FILENAME

File/directory to which output will be written; default is the terminal (STDOUT)

-p|--nopng:

In HTML output mode, skip generation of PNG graphics for each gene locus

-s|--summary:

Only print summary statistics, do not print individual comparisons

-w|--overwrite:

Force overwrite of any existing output files

-x|--refrlabel: STRING

Optional label for reference annotations

-y|--predlabel: STRING

Optional label for prediction annotations

Filtering options:

-k|--makefilter

Create a default configuration file for filtering reported results and quit, performing no comparisons

-r|--filterfile: STRING

Use the indicated configuration file to filter reported results;

-t|--maxtrans: INT

Maximum transcripts allowed per locus; use 0 to disable limit; default is 32