bgziplike

bgziplike is a term used in bioinformatics to describe an interface or implementation that mimics the behavior of BGZF, the Blocked GNU Zip Format used for compressed data with random access. A bgziplike component provides blockwise compression and decompression with the ability to seek to or read specific blocks without decompressing the entire file. The goal is to offer a compatible API and data layout so software that relies on BGZF semantics can operate against alternative backends.

Purpose and scope

BGZF is central to many genomics formats, such as BAM, VCF, and tab-delimited index files produced by Tabix. A bgziplike library or module aims to enable interchangeable backends, testing, or experimentation with different compression strategies, while preserving the general interface and access patterns expected by existing tools.

Key features

A bgziplike implementation typically supports streaming read and write of compressed data, block-level access, and the use of random-access indices to locate data within the stream. It often provides language bindings or APIs that resemble those of established BGZF libraries, enabling integration into pipelines and tools written in C, C++, Python, or other languages.

Compatibility and considerations

A true bgziplike component should strive for compatibility with tools that expect BGZF behavior. However, exact compatibility may vary in areas such as block boundaries, indexing formats, or metadata handling. Users should verify tool interoperability when substituting a bgziplike backend for a standard BGZF implementation.

See also

BGZF, BGZIP, HTSlib, Tabix, BAM, VCF.