NAME

       gaeval  -  calculate  coverage  and  intergrity scores for gene models based on transcript
       alignments

SYNOPSIS

       gaeval [options] alignments.gff3 genes.gff3 [moregenes.gff3 ...]

DESCRIPTION

       Basic options:

       -h|--help
              print this help message and exit

       -v|--version
              print version number and exit

              Weights for calculating integrity score (must add up to 1.0):

       -a|--alpha: DOUBLE
              introns confirmed, or % expected CDS length for single-exon genes; default is 0.6

       -b|--beta: DOUBLE
              exon coverage; default is 0.3

       -g|--gamma: DOUBLE
              % expected 5' UTR length; default is 0.05

       -e|--epsilon: DOUBLE
              % expected 3' UTR length; default is 0.05

              Expected feature lengths for calculating integrity score:

       -c|--exp-cds: INT
              expected CDS length (in bp); default is 400

       -5|--exp-5putr: INT
              expected 5' UTR length; default is 200

       -3|--exp-3putr: INT
              expected 3' UTR length; default is 100