Broken functionality (from_flatfile) in get_manta_sv

morinlab / GAMBLR

Set of standardized functions to operate with genomic data

https://morinlab.github.io/GAMBLR/

MIT License

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Broken functionality (from_flatfile) in get_manta_sv #74

Closed rdmorin closed 2 years ago

rdmorin commented 2 years ago

I haven't investigated the cause of this issue. I wonder if this ever worked properly in the first place. We definitely need all functions to work with the from_flatfile option and TRUE should become the new default once it does

unannotated_sv = get_manta_sv(from_flatfile = TRUE) 
Error in read_tsv(sv_file, col_types = "cnncnncnccccnnnnccc", col_names = cnames) : 
  object 'cnames' not found

rdmorin commented 2 years ago

I figured out how to fix this. It'll be fixed in my next PR. I just had to make the cnames variable global