Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: gatk-bwamem-jni
Source: https://github.com/broadinstitute/gatk-bwamem-jni/
Files-Excluded: gradle
                gradlew
Files-Excluded-bwa-apache2: bwakit
                            bwa.1
                            .gitignore
                            *.pl
                            .travis.yml
Comment: Excluding the gradle jar and cruft in the bwa component.

Files: *
Copyright: 2017 Broad Institute
License: BSD-3-clause

Files: bwa-apache2/*
Copyright: 2008 Genome Research Ltd (GRL).
License: Apache-2.0

Files: bwa-apache2/bntseq.c
       bwa-apache2/bntseq.h
       bwa-apache2/bwt.h
       bwa-apache2/bwt.c
       bwa-apache2/bwtindex.c
Copyright: 2008 Genome Research Ltd (GRL).
License: Apache-2.0

Files: bwa-apache2/is.c
Copyright: 2008 Yuta Mori
License: Expat

Files: bwa-apache2/kbtree.h
Copyright: 1997-2001 John-Mark Gurney
           2008-2009 Attractive Chaos <attractor@live.co.uk>
License: BSD-2-Clause

Files: bwa-apache2/khash.h
       bwa-apache2/kseq.h
       bwa-apache2/ksort.h
       bwa-apache2/ksw.c
       bwa-apache2/kvec.h
Copyright: 2008-2011 Attractive Chaos <attractor@live.co.uk>
License: Expat

Files: bwa-apache2/utils.c
       bwa-apache2/utils.h
Copyright: 2008 Genome Research Ltd (GRL).
License: Expat

Files: debian/*
Copyright: 2022 Pierre Gruet <pgt@debian.org>
License: BSD-3-clause

License: BSD-3-clause
 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 copyright holder 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.

License: Apache-2.0
 On Debian systems the full text of the Apache-2.0 license can be found in
 /usr/share/common-licenses/Apache-2.0.

License: Expat
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to
 deal in the Software without restriction, including without limitation the
 rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
 sell copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 .
 The above copyright notice and this permission notice shall be included in
 all copies or substantial portions of the Software.
 .
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
 IN THE SOFTWARE.

License: BSD-2-Clause
 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.
 .
 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 HOLDERS 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.
