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immunomind / immunarch

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
https://immunarch.com
Apache License 2.0
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repLoad failing to load in TRUST4 data #383

Closed sammurray13 closed 1 year ago

sammurray13 commented 1 year ago

Hi,

I have been trying to load in TRUST4 _report.tsv data into immunarch, using the repLoad function. As per some of the other bug reports, i loaded in the dev version of immunarch (using devtools::install_github("immunomind/immunarch", ref="dev")) to attempt to overcome any issues with loading in TRUST4 data. However, when i try and load in the data I get this error message:

== Step 1/3: loading repertoire files... ==

Processing "" ... -- [1/1] Parsing "inputs/TRUST_outs/IDT0097report.tsv" -- vdjtools Error in vroom(file, delim = delim %||% col_types$delim, col_names = col_names, :
bad value

and the data does not load in.

Attached is a data sample for reproducing the error: IDT0097_report.txt

Using immunarch version 1.0.0 in R version 4.2.2 (2022-10-31)

Any help you can offer would be very much appreciated. Thanks, Sam

sammurray13 commented 1 year ago

Hi,

This appears to a problem with vroom/readr. I was able to fix the problem by running readr::local_edition(1) prior to running the function as per https://github.com/tidyverse/vroom/issues/519#issuecomment-1764613014

Thanks, Sam