count_dbs_contexts() error

[ThomasGro]

I observe an error when dealing with DBS.
It seems the get_dbs_context() is not working as expected on the first GRL entry, as the test and context genomic ranges look identical.

test=MutationalPatterns::read_vcfs_as_granges(vcf_file, sample_name, ref_genome, type = "dbs")
context=MutationalPatterns::get_dbs_context(test)
counts=MutationalPatterns::count_dbs_contexts(context)
Error in purrr::map() at MutationalPatterns/R/count_dbs_contexts.R:41:5:
ℹ In index: 1.
ℹ With name: sample1.
Caused by error:
! There are some REF or ALT bases, that do not belong to any of the categories.
Did you forget to use 'get_dbs_context()'?
Run rlang::last_trace() to see where the error occurred.

rlang::last_trace(drop = F)
<error/purrr_error_indexed>
Error in purrr::map() at MutationalPatterns/R/count_dbs_contexts.R:41:5:
ℹ In index: 1.
ℹ With name: sample1.
Caused by error:
! There are some REF or ALT bases, that do not belong to any of the categories.
Did you forget to use 'get_dbs_context()'?

---

Backtrace:
▆

1. ├─MutationalPatterns::count_dbs_contexts(context)
2. │ └─purrr::map(vcf_list, .count_dbs_contexts_gr, categories) at MutationalPatterns/R/count_dbs_contexts.R:41:5
3. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
4. │ ├─purrr:::with_indexed_errors(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ ├─purrr:::call_with_cleanup(...)
7. │ └─MutationalPatterns (local) .f(.x[[i]], ...)
8. │ └─base::stop(...) at MutationalPatterns/R/count_dbs_contexts.R:90:5
9. └─base::.handleSimpleError(...)
10. └─purrr (local) h(simpleError(msg, call))

11. └─cli::cli_abort(...)
    

12.   └─rlang::abort(...)
    

I attaches the R data files in a ZIP archive for test, context, and counts for you to reproduce my error.
I hope that helps.

Thank you for your support.

dbs_error_example.zip

[pdiakumis]

Error sounded familiar - issue #56 might be useful.