This adds the MRCA time and num path nodes to the export_recombinants function. However, I want to also plot the times etc for non-HMM-consistent recombination nodes, and for nodes with > 2 parents (displayed in different point colours in the plot), so I have added the extra params restrict_to_hmm_consistent (default True) and max_num_parents (default 2) to the function call. When these are used, a slightly different set of columns are returned, as some do not make sense any more.
If this is too confusing, I could create a different export function instead, for the MRCA data. However, I think in the future we might well want to grab information for recombination nodes with multiple breakpoints, so the flexibility seems sensible to me.
This adds the MRCA time and num path nodes to the
export_recombinantsfunction. However, I want to also plot the times etc for non-HMM-consistent recombination nodes, and for nodes with > 2 parents (displayed in different point colours in the plot), so I have added the extra paramsrestrict_to_hmm_consistent(defaultTrue) andmax_num_parents(default2) to the function call. When these are used, a slightly different set of columns are returned, as some do not make sense any more.If this is too confusing, I could create a different export function instead, for the MRCA data. However, I think in the future we might well want to grab information for recombination nodes with multiple breakpoints, so the flexibility seems sensible to me.