Merge pull request #6 from standage/master

Replaced --emptyseqs with --skipends
gffTidy forced ID scheme removed, primary_transcript added as default feature, feature list overwrites default features, off by 1 gene in reporting function, produces gt compliant gff3
Merge pull request #8 from jfdenton/master

gffTidy writeGene barebones
multi-feature cds fix
Merge pull request #9 from jfdenton/master

multi-feature cds fix
Merge branch 'master' of https://github.com/BrendelGroup/AEGeAn