Man page - parseval(1)

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PARSEVAL

NAME
SYNOPSIS
DESCRIPTION

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