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Updated loop handling to match pedtools v2.11.0, including support for founder and repeated loop breakers.
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Improved likelihood calculations for looped pedigrees, with lower memory usage.
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Improved peeling algorithm, including single-child shortcuts and several minor optimisations.
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Added optional peeling diagnostics in
likelihood()andlikelihood2(), activated by.diagnostics = TRUE. -
Fixed edge case bugs in
likelihood2()involvinglogbase. -
Improved
likelihoodMerlin(), including better parsing of MERLIN output and handling of "bad inheritance" messages. -
Updated documentation of
likelihood().