Prevent spliced in-frame stop codons and allow spliced start codons

[MarioStanke]

• Extend the (n=15 states) architecture to allow the prevention of spliced stop codons.
  • Ask Mario to for a solution architecture from an exam question on genome analysis.
  • Share the parameters for the embedding emissions, so that no new parameters need to be learned and a choice between the two architectures can be made at inference time.
• Extend the architecture for spliced start codons, Agt ... ag GT or ATgt... ag G. This probably can be used with benefit only after RNA-Seq integration has been implemented.
• A simpler and faster model is chosen at first during inference. If spliced stop codons occur. The region or tile can be reannotated with the slower model that enforces structures without spliced stop codons.