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Support for vbz compression #144

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jonah-lc opened this issue Apr 10, 2024 · 2 comments
Open

Support for vbz compression #144

jonah-lc opened this issue Apr 10, 2024 · 2 comments

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@jonah-lc
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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
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Author

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;
nanoporetech/vbz_compression#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
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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

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