reference haplotypes reanalyzed but missing in the <ouput>.msp.tsv file

[sroliveiraa]

Dear Mark Koni Wright,

I ran rfmix2 with the options --reanalyze-reference and -e 3 to account for some admixture in my reference haplotypes.
While the .rfmix.Q display the global ancestry for the references, the most likely assignment of subpopulations per CRF point for the references is not printed in the .msp.tsv file.

Is there any way to print that information?
If not implemented, could you possibly add that feature? I think it would benefit other users too.

Thank you very much!

Best regards,
Sandra