Straw: rapidly stream data from .hic files

Straw is library which allows rapid streaming of contact data from .hic files. This repository contains source code for the C++, R, Python, and MATLAB versions of Straw.

• For the Java version, see: https://github.com/aidenlab/java-straw/
• For the Javascript version, see: https://github.com/igvteam/hic-straw/

There are two Python versions - a pure Python flavor and one which wraps the C++ code with pybind11. The former version has been deprecated in favor of using the pybind11 version, which is much faster.

• For archival purposes, the pure python version has been moved to: https://github.com/aidenlab/pystraw

A Jupyter notebook example of using straw can be found here: https://aidenlab.gitbook.io/juicebox/accessing-raw-data

Install straw for python

Use pip install hic-straw. If you want to build from the source code, you must have pybind11 installed. Clone the library and cd into the straw/ directory. Then pip install ./pybind11_python.

Compile straw for C++

g++ -std=c++0x -o straw main.cpp straw.cpp -lcurl -lz

You must have cURL installed. Please see the wiki for more documentation.

For questions, please use the Google Group.

Ongoing development work is carried out by Muhammad S. Shamim. Past contributors include Neva C. Durand and many others.

If you use this tool in your work, please cite

Neva C. Durand, James T. Robinson, Muhammad S. Shamim, Ido Machol, Jill P. Mesirov, Eric S. Lander, and Erez Lieberman Aiden. “Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom.” Cell Systems 3(1), 2016.