Package 'Rzarrs'

Report Rzarrs codec capabilities

Description

With no argument, returns the codecs compiled into this Rzarrs build. When passed a ZarrArray, returns support status for the codecs declared by that array, including nested sharding codecs.

Usage

codec_capabilities(x = NULL)

Arguments

x	Optional ZarrArray.

Value

A named list with codec and supported vectors.

---

Plan R materialization for a Zarr dtype

Description

Plan R materialization for a Zarr dtype.

Usage

dtype_plan(dtype)

Arguments

dtype

Character scalar dtype name.

Details

High-precision extension dtypes such as float128, decimal128, and decimal256 are planned as lossy R double values. Actual reading still depends on a registered binary-layout data type materializer because these are extension dtypes, not core built-in zarrs element types.

Value

A named list describing the planned R materialization.

---

Zarr array handle

Description

A handle to a single Zarr array within a store. Arrays can be opened from a local store (ZarrStore) or an object-store backend (ZarrObjectStore).

Indexing follows R conventions: indices are 1-based and inclusive on both ends.

Constructors

ZarrArray$open(store, path)

Open from a local ZarrStore.

store

A ZarrStore object.

path

Character scalar. Array path within the store, e.g. "/" for the root array.

ZarrArray$open_object_store(store, path)

Open from a ZarrObjectStore. Same arguments as above but store is a ZarrObjectStore.

Methods

$ndim()

Number of dimensions (integer scalar).

$shape()

Array shape (integer vector, one element per dimension).

$chunk_shape()

Chunk shape (integer vector), or NULL for irregular chunk grids.

$dtype()

Data type name in Zarr V3 canonical form, e.g. "float32", "int32", "bool" (character scalar).

$dimension_names()

Dimension names (character vector), or NULL if none are stored.

$metadata_json()

Full array metadata as pretty-printed JSON (character scalar).

$retrieve(starts = NULL, ends = NULL)

Read array data into R.

starts

Integer vector of 1-based start indices (one per dimension), or NULL to start at the first element.

ends

Integer vector of 1-based inclusive end indices (one per dimension), or NULL to include the last element.

Returns a vector of the appropriate R type (integer, double, or logical) with a dim attribute set to the shape of the requested region. Data are returned in R (Fortran / column-major) order so that standard R array indexing works as expected.

See Also

ZarrStore, ZarrObjectStore

Examples

zarr_path <- system.file("testdata", "int32.zarr", package = "Rzarrs")
arr <- ZarrArray$open(ZarrStore$open(zarr_path), "/")

arr$ndim()        # 2
arr$shape()       # c(4L, 6L)
arr$dtype()       # "int32"

# Full array
full <- arr$retrieve()
dim(full)         # c(4L, 6L)
full[1, 6]        # 6

# Subset: rows 1-2, cols 1-3
sub <- arr$retrieve(c(1L, 1L), c(2L, 3L))
dim(sub)          # c(2L, 3L)

---

A handle to a Zarr group (root or sub-group) within a store.

Description

Groups may contain arrays and/or sub-groups. Use '$attributes()' to read the group's JSON attributes as a native R list, and '$children()' to list the immediate child nodes.

Usage

ZarrGroup

Format

An object of class Rzarrs::ZarrGroup__bundle (inherits from savvy_Rzarrs__sealed) of length 2.

---

Object-store Zarr backend (S3, GCS, Azure, HTTP/HTTPS)

Description

A handle to a Zarr store backed by any URL scheme supported by the object_store crate: s3://, gs://, az://, https://, or file:///. URLs ending in ile.zarr.zip or ile.zip are opened as zip objects when the Rust ilezip feature is enabled.

Credentials are read automatically from the standard environment variables for each provider (the same ones used by the AWS CLI, gsutil, azcopy, etc.). No credentials are ever passed as R objects.

Constructor

ZarrObjectStore$open(url)

Open an object-store backend.

url

Character scalar. Store URL, e.g. "s3://my-bucket/path/to/store.zarr", "s3://my-bucket/path/to/store.zarr.zip", or "https://example.com/store.zarr".

Returns a ZarrObjectStore object.

Methods

$url()

Return the URL passed to open() as a character scalar.

Credentials

Set the relevant environment variables before calling open():

AWS S3

AWS_ACCESS_KEY_ID, AWS_SECRET_ACCESS_KEY, AWS_REGION, AWS_ENDPOINT_URL

Google GCS

GOOGLE_APPLICATION_CREDENTIALS

Azure Blob

AZURE_STORAGE_ACCOUNT, AZURE_STORAGE_ACCESS_KEY

See Also

ZarrStore, ZarrArray

Examples

## Not run: 
store <- ZarrObjectStore$open("s3://my-bucket/my.zarr")
arr   <- ZarrArray$open_object_store(store, "/")
arr$shape()

## End(Not run)

---

Local Zarr filesystem store

Description

A handle to a Zarr store rooted at a local directory. Use ZarrStore$open(path) to create one, then pass it to ZarrArray$open(store, path) to open individual arrays.

Constructor

ZarrStore$open(path)

Open a local Zarr store.

path

Character scalar. Path to the ‘.zarr’ directory.

Returns a ZarrStore object.

Methods

$path()

Return the store root path as a character scalar.

See Also

ZarrObjectStore, ZarrArray

Examples

zarr_path <- system.file("testdata", "int32.zarr", package = "Rzarrs")
store <- ZarrStore$open(zarr_path)
store$path()

---

High-level VCF Zarr reader

Description

'ZarrVcf$open(x)' opens a VCF Zarr store (spec versions 0.1–0.4) and returns an instance with methods to access variant, sample, and genotype data. Genotypes use the VCF Zarr integer encoding: allele indexes are 0-based, '-1' is a missing allele ('.' in VCF), and '-2' is the array fill sentinel.

Usage

ZarrVcf

Format

An object of class Rzarrs::ZarrVcf__bundle (inherits from savvy_Rzarrs__sealed) of length 3.

Methods

'$open(x)'

Open a VCF Zarr store from a path, URL, 'ZarrStore', or 'ZarrObjectStore'.

'$version()'

VCF Zarr spec version string.

'$n_variants()', '$n_samples()'

Number of variants and samples.

'$samples()', '$contigs()', '$filters()'

Character vectors of sample IDs, contig names, filter IDs.

'$fields()'

Available array names.

'$variant_position()', '$variant_contig()', '$variant_allele()'

Per-variant data.

'$genotypes(variants, samples)'

3-D array (variants × samples × ploidy) of integer genotypes using VCF Zarr '-1'/'-2' sentinel values.

'$call_genotype_phased(variants, samples)'

Boolean phased matrix.

'$variant(name)', '$call(name)'

Generic accessor for 'variant_<name>' / 'call_<name>' arrays.

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