NAME

       parseval - comparative analysis of two alternative sources of annotation

SYNOPSIS

       parseval [options] reference.gff3 prediction.gff3

DESCRIPTION

       Basic options:

       -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