The main hap.py code (in the src subfolder) is distributed under the
simplified BSD license.

The full text can be found here:

https://github.com/Illumina/licenses/blob/master/Simplified-BSD-License.txt

-------------------------------------------------------------------------------
Copyright (c) 2010-2015 Illumina, Inc.
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this
   list of conditions and the following disclaimer.

2. 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.

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.
-------------------------------------------------------------------------------

The dependencies supplied in the external subfolder are covered by their own
respective licenses as follows (original license text included in the
respective source files / tarballs):

*   Htslib 1.3 (MIT license -
    https://github.com/samtools/htslib/blob/develop/LICENSE)
*   bcftools 1.3 (MIT license -
    https://github.com/samtools/bcftools/blob/develop/LICENSE)
*   samtools 1.3 (MIT license -
    https://github.com/samtools/samtools/blob/develop/LICENSE)
*   Klib/ksw (from https://github.com/attractivechaos/klib -- MIT license)
*   JsonCPP (MIT license --
    https://github.com/open-source-parsers/jsoncpp/blob/master/LICENSE)
*   GetGitRevisionDescription.cmake from
    https://github.com/rpavlik/cmake-modules/blob/master/GetGitRevisionDescription.cmake
    Copyright Iowa State University 2009-2014
    Distributed under the Boost Software License, Version 1.0.
    (See http://www.boost.org/LICENSE_1_0.txt)
*   Python virtualenv: MIT-like
    (https://raw.githubusercontent.com/pypa/virtualenv/master/LICENSE.txt)

Further dependencies (to be installed by the user of this software):

*   Python/Pandas: BSD-compatible
    (http://pandas.pydata.org/pandas-docs/stable/overview.html#license)
*   Python/PySAM: MIT license (https://github.com/pysam-developers/pysam)
*   bx-python: Copyright (c) 2005-2015 The Pennsylvania State University
               Copyright (c) 2013-2015 The Johns Hopkins University
               (https://bitbucket.org/james_taylor/bx-python)
*   Boost C++ library: Boost software license
    (http://www.boost.org/users/license.html)
*   RTGtools for variant comparison: Simplified BSD license,
    Copyright (c) 2015, Real Time Genomics Limited
    https://github.com/RealTimeGenomics/rtg-tools/blob/ga4gh-test/LICENSE.txt
    https://github.com/RealTimeGenomics/rtg-tools/tree/ga4gh-test
