The ARG-Needle docs imply that mutations can be stored on the ARG, e.g. they say "arg2tskit does convert mutations.". However, when I run ARG-needle on real data, e.g. via the arg_needle_prepare_example command, the resulting .argn file does not seem to contain any mutations:
import arg_needle_lib
argneedle_arg = arg_needle_lib.deserialize_arg("example.argn")
arg_needle_lib.get_mutations_matrix(argneedle_arg)Gives:
RuntimeError: /Users/runner/work/arg-needle-lib/arg-needle-lib/src/arg_utils.cpp:714: Need pre-existing mutations to run! Try generate_mutations_and_keep.
Note that there is no arg_needle_lib.generate_mutations_and_keep function (although there is an arg_needle_lib.generate_mutations function.
How can I place the mutations used during ARG inference on the ARG (and can this detail be added to the docs?)
The ARG-Needle docs imply that mutations can be stored on the ARG, e.g. they say "
arg2tskitdoes convert mutations.". However, when I run ARG-needle on real data, e.g. via thearg_needle_prepare_examplecommand, the resulting.argnfile does not seem to contain any mutations:Gives:
Note that there is no
arg_needle_lib.generate_mutations_and_keepfunction (although there is anarg_needle_lib.generate_mutationsfunction.How can I place the mutations used during ARG inference on the ARG (and can this detail be added to the docs?)