I've written code like this to work with overlapping genes. While most genes exist in a genome with spacers between them and their neighboring genes, sometimes

I've written code like this to work with overlapping genes. While most genes exist in a genome with spacers between them and their neighboring genes, sometimes you get pairs of genes which overlap, and there seems to be some interesting biology that happens as a consequence. Here's a package for Python that presumably uses some sort index data structure to be efficient: https://pyranges.readthedocs.io/en/latest/ https://pyranges.readthedocs.io/en/latest/