We might want to list all the breakpoints in the ARG and exclude those which were only reported in the HMM metadata. At the moment I don't think there is any way to do this from the export_recombinant_breakpoints function. The nearest is is_arg_hmm_path_length_consistent, but removing breakpoints with that set to false will also remove breakpoints on which the ARG and the HMM agree, but which are contained in a recombination node with e.g. different numbers of parents in the ARG and the HMM.
We really need a per-breakpoint measure for this, not a per recombination-node measure, I guess. It's unlikely to be many breakpoints, but I have observed some like this.
We might want to list all the breakpoints in the ARG and exclude those which were only reported in the HMM metadata. At the moment I don't think there is any way to do this from the
export_recombinant_breakpointsfunction. The nearest isis_arg_hmm_path_length_consistent, but removing breakpoints with that set to false will also remove breakpoints on which the ARG and the HMM agree, but which are contained in a recombination node with e.g. different numbers of parents in the ARG and the HMM.We really need a per-breakpoint measure for this, not a per recombination-node measure, I guess. It's unlikely to be many breakpoints, but I have observed some like this.