GTF specification should include start and stop codons

[ewallace]

I think, the input gtf to metaplots and prepare_transcripts needs start_codon and stop_codon features in order to recognize something as an annotated CDS; CDS features are not enough. Could this be added as an option in GTF_update.rst?

Importantly, could this be clarified explicitly in the gtf specification in README.md?

[zhengtaoxiao]

Yes, the genomic coordinates of start_codon and stop_codon are required for metaplots. "GTF_update" will use these two features if they are provided in the GTF file, otherwise the "prepare_transcripts" will try to infer them from the "CDS" feature. We will explain it more clearly in the next version. Thanks!