A datatype representing Infernal covariance models. This is a new representation that is incompatible with the one once found in Biobase. The most important difference is that lookups are mapped onto efficient data structures, currently PrimitiveArray.
- Each State of a covariance model has up to 6 transition scores, hence we need s*6 cells for transitions.
- Each State of a covariance has up to 16 emission scores, so we have s*16 cells for emissions, with unused cells set to a really high score.
On top of these basic structures, we then place additional high-level constructs.
pathsare allowed transitions. This can safe a check, if the transition is encoded with a forbidden score.
localEndare local entry and exit strategies. A
localBeginis a transition score to certain states, all such transitions are in
localEndis a transition score to a local end state.