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..
This file is part of khmer, https://github.com/dib-lab/khmer/, and is
Copyright (C) 2014-2015 Michigan State University
Copyright (C) 2015-2016 The Regents of the University of California.
It is licensed under the three-clause BSD license; see LICENSE.
Contact: khmer-project@idyll.org
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following
disclaimer in the documentation and/or other materials provided
with the distribution.
* Neither the name of the Michigan State University nor the names
of its contributors may be used to endorse or promote products
derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Contact: khmer-project@idyll.org
A quick guide to the khmer codebase
===================================
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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