htslurp

Warning

This is an experiment and the code is in a not-working state.

Attempt at making a noodles-based htsget client that can lazily deserialize records in memory. The aim is to provide a simple rust API with python bindings.

Context

The aim of this project is to provide a convenient interface to consume remote CRAM/BCF records over the network without storing them locally.

The noodles crate is used to fetch a binary stream from a server and construct a reader over it that can lazily instantiate records.

flowchart LR
    htsget[htsget-server] -->|bytes| Reader
    Reader -->|Cram records| python

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Development

This project requires:

• a working rust (>=1.76) and python (>=3.10) installation
• maturin
• uv
• just

To build the python package:

just build

To install the project in installable mode:

just develop