Infernal CMs.
Documentation
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.
- 1
- Each State of a covariance model has up to 6 transition scores, hence we need s*6 cells for transitions.
- 2
- 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.
- 3
-
paths
are allowed transitions. This can safe a check, if the transition is encoded with a forbidden score. - 4
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localBegin
andlocalEnd
are local entry and exit strategies. AlocalBegin
is a transition score to certain states, all such transitions are inbegins
. AlocalEnd
is a transition score to a local end state.
TODO as with other projects, we should not use Double's but Score and Probability newtypes.