Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.
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clustervars: in_params_fn and out_params_fn are not documented #11
Please, document what in_params_fn and out_params_fn is.
By looking at code, I can see that out_params_fn is an output file where the (prefix).params.json with estimated clusters is dumped and that in_params_fn is some initialization file, apparently in JSON format, from which samples and garbage variants are taken and possibly initial clusters as well. But this is not documented in --help.
From what I am reading, in_params_fn shouldn't even be a required parameter. Sample information should be already included in the ssm_fn and the other two could be/are optional.
I am more than happy to fix some of the documentation issues if you want to.
Please, document what in_params_fn and out_params_fn is.
By looking at code, I can see that
out_params_fnis an output file where the(prefix).params.jsonwith estimated clusters is dumped and thatin_params_fnis some initialization file, apparently in JSON format, from which samples and garbage variants are taken and possibly initial clusters as well. But this is not documented in--help.From what I am reading,
in_params_fnshouldn't even be a required parameter.Sampleinformation should be already included in thessm_fnand the other two could be/are optional.I am more than happy to fix some of the documentation issues if you want to.