pybedtools development model

pybedtools is very much an open-source project. We do all of our development in a public github repository ( Initially Ryan Dale created pybedtools as a wrapper for the BEDTools command-line that allowed whole-file operations (e.g., intersecting two BED files). At around the same time, Aaron Quinlan began bedtools-python, a Cython wrapper to the BEDTools C++ API which allowed per-line operations. After using both libraries, Brent Pedersen made an initial attempt to merge the two libraries so that one could do a whole-file operation and then iterate line-wise over the result.

All three authors – especially Ryan – then worked on the integration and further improvements. We often discussed individual commits and design decisions using the github interface. These discussions (often visible in github tickets such as facilitated the continued collaboration, and our daily use of the library have shaped pybedtools into what it is today.

As three independent bioinformaticians who have not previously worked together, using github as a place for discussing design decisions and coding standards has been invaluable.