All functions that internally call get_gambl_metadata() should have been updated to require the user specify the seq_type of the sample when not providing the metadata. This is required because the function cannot call get_gambl_metadata() with the right seq_type otherwise. Currently, if a user runs get_ssm_by_sample and specifies a sample_id from any "capture" data set then the function fails unless they also provide the metadata. The fixes for this are twofold:
1) make seq_type a required argument UNLESS the user specifies the argument these_samples_metadata
2) this_sample_id should not be a required argument because, as we do for many functions, this id can be pulled from these_samples_metadata. Hence, the function should require the user specify one of these_samples_metadata or this_sample_id and use whichever one appropriately
Here's an example where the function is currently failing:
slms3_var_calls <- get_ssm_by_sample(
this_sample_id = "PA001",
augmented = FALSE,
min_read_support = 3
)
Error in if (pair_status == "unmatched") { : argument is of length zero
All functions that internally call get_gambl_metadata() should have been updated to require the user specify the seq_type of the sample when not providing the metadata. This is required because the function cannot call get_gambl_metadata() with the right seq_type otherwise. Currently, if a user runs get_ssm_by_sample and specifies a sample_id from any "capture" data set then the function fails unless they also provide the metadata. The fixes for this are twofold:
1) make seq_type a required argument UNLESS the user specifies the argument these_samples_metadata 2) this_sample_id should not be a required argument because, as we do for many functions, this id can be pulled from these_samples_metadata. Hence, the function should require the user specify one of these_samples_metadata or this_sample_id and use whichever one appropriately
Here's an example where the function is currently failing: