.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH GAEVAL "1" "January 2016" "gaeval 0.15.1" "User Commands"
.SH NAME
gaeval \- calculate coverage and intergrity scores for gene models based on transcript alignments
.SH SYNOPSIS
.B gaeval
[\fI\,options\/\fR] \fI\,alignments.gff3 genes.gff3 \/\fR[\fI\,moregenes.gff3 \/\fR...]
.SH DESCRIPTION
Basic options:
.TP
\fB\-h\fR|\-\-help
print this help message and exit
.TP
\fB\-v\fR|\-\-version
print version number and exit
.IP
Weights for calculating integrity score (must add up to 1.0):
.TP
\fB\-a\fR|\-\-alpha: DOUBLE
introns confirmed, or % expected CDS length for
single\-exon genes; default is 0.6
.TP
\fB\-b\fR|\-\-beta: DOUBLE
exon coverage; default is 0.3
.TP
\fB\-g\fR|\-\-gamma: DOUBLE
% expected 5' UTR length; default is 0.05
.TP
\fB\-e\fR|\-\-epsilon: DOUBLE
% expected 3' UTR length; default is 0.05
.IP
Expected feature lengths for calculating integrity score:
.TP
\fB\-c\fR|\-\-exp\-cds: INT
expected CDS length (in bp); default is 400
.TP
\fB\-5\fR|\-\-exp\-5putr: INT
expected 5' UTR length; default is 200
.TP
\fB\-3\fR|\-\-exp\-3putr: INT
expected 3' UTR length; default is 100