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

**gaeval** [

*options*]

*alignments.gff3 genes.gff3
*[

*moregenes.gff3 *...]

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