tatami_tiledb::SparseMatrixOptions Struct Reference

Options for sparse TileDB extraction. More...

#include <SparseMatrix.hpp>

Public Attributes
size_t	maximum_cache_size = 100000000
bool	require_minimum_cache = true

Detailed Description

Options for sparse TileDB extraction.

Note that more TileDB-specific options can be set by passing in a custom tiledb::Context option to the SparseMatrix constructor.

Member Data Documentation

maximum_cache_size

size_t tatami_tiledb::SparseMatrixOptions::maximum_cache_size = 100000000

Size of the in-memory cache in bytes.

We cache all tiles required to read a row/column during a tatami::SparseExtractor::fetch() or tatami::SparseExtractor::Fetch() call. This allows us to re-use the cached tiles when adjacent rows/columns are requested, rather than re-reading them from disk.

Larger caches improve access speed at the cost of memory usage. Small values may be ignored if require_minimum_cache is true.

require_minimum_cache

bool tatami_tiledb::SparseMatrixOptions::require_minimum_cache = true

Whether to automatically enforce a minimum size for the cache, regardless of maximum_cache_size. This minimum is chosen to ensure that all tiles overlapping one row (or a slice/subset thereof) can be retained in memory, so that the same tiles are not repeatedly re-read from disk when iterating over consecutive rows/columns of the matrix.

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The documentation for this struct was generated from the following file:

• tatami_tiledb/SparseMatrix.hpp