Empty tables and nullable

[gtca]

Should make it possible to read more files out there as in #14

[ilia-kats]

perhaps add a comment referencing hhoeflin/hdf5r#118 so we know what this workaround is for (and can remove it in the future)

[ilia-kats]

LGTM

[DriesSchaumont]

Thanks for the PR! 🙇 When running this branch on s3://openpipelines-data/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect_mms.h5mu as described at #14 I now get the following error. I don't know if this is related to the original issue or if I should creata a new ticket. Let me know!
I appreciate you guys pointing out that one of the modalities has 0 features. I did not notice before 🤔

Error in `LayerData()`:
! `features` must be a character vector, not `NULL`.
Backtrace:
     ▆
  1. └─MuDataSeurat::ReadH5MU(par$input)
  2.   ├─Seurat::CreateSeuratObject(...)
  3.   └─SeuratObject:::CreateSeuratObject.Assay(...)
  4.     ├─SeuratObject:::CalcN(object = counts)
  5.     └─SeuratObject:::.CalcN.Assay(object = counts)
  6.       ├─SeuratObject::LayerData(object = object, layer = layer)
  7.       └─SeuratObject:::LayerData.Assay(features = NULL)
  8.         └─rlang::arg_match(...)
  9.           └─rlang:::check_character(arg, arg = error_arg, call = error_call)
 10.             └─rlang:::stop_input_type(...)
 11.               └─rlang::abort(message, ..., call = call, arg = arg)

[gtca]

Hey @DriesSchaumont,

Which version of Seurat / SeuratObject have you been using?
With Seurat_4.0.4 and SeuratObject_4.0.2 I cannot reproduce it but I suspect you see it in Seurat 5?

We haven't covered Seurat 5 changes yet — the respective changes should probably land in another PR. A new issue might be a good start? 😃

Do you think the error you see here is also related to a modality with no features?..

[DriesSchaumont]

Hi @gtca, that worked (although I could not use Seurat 4.4.0). Seurat v5 support would be great, but as you said: that would be for another PR 👍