Automated testing

AEGeAn core code

Annotation feature I/O

Status	Test
	Load correct number of features
	Infer CDS correctly from exons and start / stop codons
	Infer UTRs correctly from exons and CDS (including UTRs containing introns)
	Infer introns correctly from exons
	Infer exons correctly from CDS and (if provided) UTRs
	Infer codons correctly from CDS
	Infer genes for mRNAs without gene specified
	Sanity check: no overlap in features of the same type, or adjacent features of the same type
	Sanity check: gene has 1 or more mRNA subfeatures
	Sanity check: range of mRNA feature falls within range of its gene
	Sanity check: mRNA has 1 CDS subfeature
	Sanity check: mRNA has n - 1 intron subfeatures (n is number of exons)
	Sanity check: range of mRNA subfeatures fall within range of their mRNA
	Print functions produce valid GFF3 format

Model vectors

Status	Test
	Model vectors built correctly from single transcripts
	Model vectors built correctly from transcript cliques

Loci

Status	Test
	AgnGeneLocus objects infer coordinates correctly from added genes
	AgnGeneLocus objects correctly identify best transcript clique pairs

Filters

Status	Test
	Filter files parsed correctly
	Filters applied correctly