Update bgen2 to use cbgen

limix / bgen-reader-py

A BGEN file format reader.

MIT License

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Closed CarlKCarlK closed 4 years ago

CarlKCarlK commented 4 years ago

bgen2 now uses cbgen. It mostly uses the cbgen's main python API. In two places it uses the "lib" interface:

To put samples into memory-mapped file instead of RAM
to extract ncomb and phased info without extracting probabilities (and into memory-mapped file)

This update also includes improved coverage, error messages, and verbose messages.

CarlKCarlK commented 4 years ago

I fixed a bug, but don't know how to update the pull request. Please merge from 9a7a26e9.