A C library for accessing 2bit files. This is still a work in process. Note that functionality is mostly aimed at what will be needed in a python wrapper.
Introduction
lib2bit is a C-based library for accessing 2bit files. At the moment, only reading 2bit files is supported (there are no plans to change this, though if someone wants to submit a pull request...). Though it's unlikely to matter,
The motivation for this project is due to needing fast access to 2bit files in deepTools. Originally, we were using bx-python for this, which had the benefit of being easy to install and pretty quick. However, that wasn't compatible with python3, so we switched to twobitreader. While doing everything we needed and working under both python2 and python3, it turns out that it has terrible performance (up to 1000x slow down in computeGCBias). Since we'd like to have our cake and eat it too, I began wrote a C library for convenient 2bit access and then a python wrapper around it to work in python2 and 3.
Installation
2bit files are very simple and there are no dependencies. Simply typing make should suffice for compilation. To install into a specific path (the default is /usr/local):
make install prefix=/some/where/else
lib2bit.so and lib2bit.a will then be in /some/where/else/lib and 2bit.h in /some/where/else/include.
Example
See the test/ directory for an example of using the library.