Include the leading branch transition in the consensus graph#3
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StephenStaklinski wants to merge 1 commit intoCshlSiepelLab:mainfrom
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Added explicit sampling of the primary state (tissue) at the parent of the leading branch (which I call the origin node). Then, considered this sampled origin state in the edgewise consensus graph construction so that the output is correct if a state transition occurs on that leading branch from origin node -> root node. Lastly, added TODO comments to the dot and nexus state output functions to consider this same potential states transition and to adjust times for the leading branch height.