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