fix: reconstruction of ambiguous nucs in ancestral parsimony mode #293
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Followup of: #292 The transition from character sets to bit sets introduced some confusion in handling of ambiguous characters. Ambiguous characters correspond to multiple canonical characters, so they needed explicit disambiguation and disambiguation when using sets. With profile maps (arrays of floats) and with bitsets (~arrays of bits) this happens transparently: multiple "enabled" bits denote canonical components of an ambiguous character. Here I introduce precalculated `char_to_set` and `set_to_char` maps, which, allow to resolve particular combinations of bits from and to characters. This is similar to how profile maps operate, but with bits (0s and 1s) rather than floating point values. This allows the remaining test for parsimony reconstruction to pass.
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Followup of: #292
The transition from character sets to bit sets introduced some confusion in handling of ambiguous characters. Ambiguous characters correspond to multiple canonical characters, so they needed explicit disambiguation and disambiguation when using sets. With profile maps (arrays of floats) and with bitsets (~arrays of bits) this happens transparently: multiple "enabled" bits denote canonical components of an ambiguous character.
Here I introduce precalculated
char_to_setandset_to_charmaps, which allow to resolve particular combinations of bits from and to characters. This is similar to how profile maps operate, but with bits (0s and 1s) rather than floating point values.This allows the remaining test for parsimony reconstruction to pass.