search

grimbough / rhdf5

Package providing an interface between HDF5 and R
http://bioconductor.org/packages/rhdf5
61 stars 22 forks source link

Support for vbz compression #144

Open jonah-lc opened 6 months ago

jonah-lc commented 6 months ago

Hi, I use this excellent package as part of a workflow for analysis on .fast5 data from Oxford Nanopore. More recent data uses vbz compression instead of gzip (see https://github.com/nanoporetech/vbz_compression?tab=readme-ov-file) and as a result I can no longer parse the datasets with h5read, throwing an error about the compression; " Error: Unable to read dataset. Not all required filters available. Missing filters: vbz " Is it possible for me to build rhd5 against my systems vbz libraries in anyway? All the best.

jonah-lc commented 6 months ago

Ignore me, I've got this working just fine now. It may have just been an updates issue, as I had a lot to do, but for anyone else who is struggling, this link helped; https://github.com/nanoporetech/vbz_compression/issues/21 as well as (obviously) installing the vbz package from the ONT repository, and making sure rhdf5filters and Rhdf5lib were installed from BioConductor. Anyway, thanks for making this super useful package.

grimbough commented 6 months ago

Glad you got it sorted. rhdf5filters has only supported VBZ in the most recent release version, so you have to be using Bioconductor 3.18 and rhdf5filters 1.14.0