A quick guide to the khmer codebaseΒΆ

The CHANGELOG.md file lists major changes to the codebase with each version, with the most recent version first.

The include/ directory contains all C++ and C headers. The core C++ library is under include/oxli, and the CPython wrapper is under include/khmer.

The src directory contains all of the C++ and CPython code. This structure corresponds to the one in include. The main CPython module is built in src/khmer/_cpy_khmer.hh.

The khmer/ directory contains the khmer package (khmer/__init__.py, etc) and experimental Cython bindings under khmer/_oxli.

The scripts/ and sandbox/ directory contain Python command-line scripts.

The tests/ directory contains all of the tests. Each test is a function in one of the tests/test*.py files.

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