Add experimental support for Zarr format 3 #42
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tomwhite
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tomwhite
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Sep 25, 2025
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| This specification depends on definitions and terminology from [The Variant Call Format Specification, VCFv4.3 and BCFv2.2](https://samtools.github.io/hts-specs/VCFv4.3.pdf), | ||
| and [Zarr storage specification version 2](https://zarr.readthedocs.io/en/stable/spec/v2.html). | ||
| and [Zarr storage specification version 2](https://zarr.readthedocs.io/en/stable/spec/v2.html) or [Zarr core specification version 3](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) [experimental]. |
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Marked as "experimental" until we've got experience using implementations of this. (Also, I'm not planning on merging this soon.)
tomwhite
commented
Sep 25, 2025
| | `bool` | `\|b1` | `bool` | Flag | | ||
| | `int` | `<i1`, `<i2`, `<i4`, `<i8` or `>i1`, `>i2`, `>i4`, `>i8` | `int8`, `int16`, `int32`, `int64` | Integer | | ||
| | `float` | `<f4`, `<f8` or `>f4`, `>f8` | `float32`, `float64` | Float | | ||
| | `char` | `\<U1` or `\>U1` | `string` | Character | |
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Zarr format v3 doesn't use NumPy dtypes any more, and it doesn't have a "char" type, so I've represented VCF Character as a Zarr string. This would work, but would mean that converting VCF Zarr back to VCF would be lossy in the sense that a VCF Character field would be converted back to a VCF String. This may not matter, but it could potentially be fixed by either i) adding a "char" type/fixed-length string type to Zarr, or ii) adding an attribute to VCF Zarr to record the fact that it is logically a single character.
This was referenced Sep 25, 2025
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Fixes #41