.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH PARSEVAL "1" "January 2016" "parseval 0.15.1" "User Commands"
.SH NAME
parseval \- comparative analysis of two alternative sources of annotation
.SH SYNOPSIS
.B parseval
[\fI\,options\/\fR] \fI\,reference.gff3 prediction.gff3\/\fR
.SH DESCRIPTION
Basic options:
.TP
\fB\-d\fR|\-\-debug:
Print debugging messages
.TP
\fB\-h\fR|\-\-help:
Print help message and exit
.TP
\fB\-l\fR|\-\-delta: INT
Extend gene loci by this many nucleotides;
default is 0
.TP
\fB\-V\fR|\-\-verbose:
Print verbose warning messages
.TP
\fB\-v\fR|\-\-version:
Print version number and exit
.IP
Output options:
.TP
\fB\-a\fR|\-\-datashare: STRING
Location from which to copy shared data for
HTML output (if `make install' has not yet
been run)
.TP
\fB\-f\fR|\-\-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
.TP
\fB\-g\fR|\-\-nogff3:
Do no print GFF3 output corresponding to each
comparison
.TP
\fB\-o\fR|\-\-outfile: FILENAME
File/directory to which output will be
written; default is the terminal (STDOUT)
.TP
\fB\-p\fR|\-\-nopng:
In HTML output mode, skip generation of PNG
graphics for each gene locus
.TP
\fB\-s\fR|\-\-summary:
Only print summary statistics, do not print
individual comparisons
.TP
\fB\-w\fR|\-\-overwrite:
Force overwrite of any existing output files
.TP
\fB\-x\fR|\-\-refrlabel: STRING
Optional label for reference annotations
.TP
\fB\-y\fR|\-\-predlabel: STRING
Optional label for prediction annotations
.IP
Filtering options:
.TP
\fB\-k\fR|\-\-makefilter
Create a default configuration file for
filtering reported results and quit,
performing no comparisons
.TP
\fB\-r\fR|\-\-filterfile: STRING
Use the indicated configuration file to
filter reported results;
.TP
\fB\-t\fR|\-\-maxtrans: INT
Maximum transcripts allowed per locus; use 0
to disable limit; default is 32