Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: GenomicsDB
Source: https://github.com/GenomicsDB/GenomicsDB

Files: *
Copyright: 2016-2018 Intel Corporation
License: Expat

Files: .github/resources/hadoop/hadoop-env.sh
       .travis/resources/hadoop/hadoop-env.sh
Copyright: Apache Software Foundation
License: Apache-2.0

Files: .github/scripts/*
Copyright: 2018-2022, Omics Data Automation, Inc.
License: Expat

Files: example/java/TestGenomicsDBSource.java
Copyright: 2018-2020 Omics Data Automation
License: Expat

Files: example/java/TestGenomicsDBSparkHDFS.java
Copyright: 2018 Univeristy of Caifornia, Los Angeles and Intel Corporation
License: Expat

Files: genomicsdb-htslib/*
Copyright: 2008-2020 Genome Research Ltd.
License: Expat

Files: genomicsdb-htslib/bgzf.c
       genomicsdb-htslib/htslib/bgzf.h
Copyright: 2008 Broad Institute / Massachusetts Institute of Technology
           2011-2012 Attractive Chaos <attractor@live.co.uk>
           2009-2020 Genome Research Ltd
License: Expat

Files: genomicsdb-htslib/bgzip.1
Copyright: 2018 Genome Research Limited.
           2009-2011 Broad Institute.
License: Expat

Files: genomicsdb-htslib/bgzip.c
Copyright: 2008-2009 Broad Institute / Massachusetts Institute of Technology
           2010-2019 Genome Research Ltd.
License: Expat

Files: genomicsdb-htslib/cram/*
       genomicsdb-htslib/header.c
       genomicsdb-htslib/header.h
Copyright: 2005-2020 Genome Research Ltd.
License: BSD-3-clause

Files: genomicsdb-htslib/cram/misc.h
       genomicsdb-htslib/cram/open_trace_file.c
       genomicsdb-htslib/cram/open_trace_file.h
       genomicsdb-htslib/cram/os.h
Copyright: 1993-2002 MEDICAL RESEARCH COUNCIL
License: BSD-3-clause

Files: genomicsdb-htslib/errmod.c
       genomicsdb-htslib/tabix.1
       genomicsdb-htslib/tabix.c
       genomicsdb-htslib/faidx.c
       genomicsdb-htslib/hts.c
       genomicsdb-htslib/realn.c
       genomicsdb-htslib/sam.c
       genomicsdb-htslib/tbx.c
       genomicsdb-htslib/htslib/sam.h
       genomicsdb-htslib/htslib/tbx.h
       genomicsdb-htslib/htslib/vcf.h
       genomicsdb-htslib/vcf.5
Copyright: 2008-2020 Genome Research Ltd.
           2009-2013 Broad Institute.
License: Expat

Files: genomicsdb-htslib/faidx.5
       genomicsdb-htslib/sam.5
       genomicsdb-htslib/m4/*
       genomicsdb-htslib/test/*
Copyright: 2008-2020 Genome Research Ltd.
License: Expat

Files: genomicsdb-htslib/htslib/hts.h
Copyright: 2012-2020 Genome Research Ltd.
           2010-2012 Broad Institute.
           2003-2010 Heng Li <lh3@live.co.uk>
License: Expat

Files: genomicsdb-htslib/htslib/kfunc.h
       genomicsdb-htslib/kfunc.c
Copyright: 2011 Attractive Chaos <attractor@live.co.uk>
           2010-2014 Genome Research Ltd.
License: Expat

Files: genomicsdb-htslib/htslib/khash.h
       genomicsdb-htslib/htslib/klist.h
       genomicsdb-htslib/htslib/kseq.h
       genomicsdb-htslib/htslib/kstring.h
       genomicsdb-htslib/kstring.c
Copyright: 2013-2020 Genome Research Ltd.
           2008-2011 Attractive Chaos <attractor@live.co.uk>
License: Expat

Files: genomicsdb-htslib/htslib/knetfile.h
       genomicsdb-htslib/htslib/ksort.h
       genomicsdb-htslib/knetfile.c
Copyright: 2008-2019 Genome Research Ltd (GRL).
License: Expat

Files: genomicsdb-htslib/m4/hts_prog_cc_warnings.m4
Copyright: 2015-2017 Genome Research Limited
           2002 Ville Laurikari
License: FSFAP

Files: genomicsdb-htslib/m4/pkg.m4
Copyright: 2012-2015 Dan Nicholson <dbn.lists@gmail.com>
           2004 Scott James Remnant <scott@netsplit.com>.
License: GPL-2+ with Autoconf-data exception

Files: genomicsdb-htslib/md5.c
       genomicsdb-htslib/os/lzma_stub.h
Copyright: 2001 Alexander Peslyak
License: public-domain

Files: genomicsdb-htslib/os/rand.c
Copyright: 1993 Martin Birgmeier
License: Other

Files: genomicsdb-htslib/probaln.c
Copyright: 2016-2017 Genome Research Ltd.
           2003-2010 Heng Li <lh3lh3@live.co.uk>
License: Expat

Files: genomicsdb-htslib/test/fuzz/*
Copyright: 2019 Genome Research Ltd.
           2018 Google LLC.
License: Expat

Files: genomicsdb-htslib/test/plugins-dlhts.c
       genomicsdb-htslib/test/test_kfunc.c
       genomicsdb-htslib/test/with-shlib.sh
Copyright: 2020 University of Glasgow.
License: Expat

Files: genomicsdb-htslib/test/test_bgzf.c
Copyright: 2017-2019 Genome Research Ltd
License: Expat

Files: genomicsdb-htslib/test/test_view.c
Copyright: 2010-2020 Genome Research Ltd.
           2009-2013 Broad Institute.
License: Expat

Files: genomicsdb-htslib/vcf.c
Copyright: 2014 Intel Corporation.
           2012-2020 Genome Research Ltd.
           2012-2013 Broad Institute.
License: Expat

Files: genomicsdb-tiledb/*
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/*
Copyright: 2016 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/array/array_iterator.h
       genomicsdb-tiledb/core/include/misc/utils.h
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/c_api/*
Copyright: 2019-2022 Omics Data Automation Inc.
           2018-2019 Omics Data Automation Inc. and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/c_api/tiledb.h
       genomicsdb-tiledb/core/include/expressions/*
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/c_api/tiledb_constants.h
Copyright: 2016 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/codec/*
       genomicsdb-tiledb/core/include/misc/error.h
       genomicsdb-tiledb/core/include/storage_manager/*
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: genomicsdb-tiledb/core/include/misc/trace.h
Copyright: 2018 University of California, Los Angeles and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/misc/uri.h
Copyright: 2019-2022 Omics Data Automation, Inc.
           2018 University of California, Los Angeles and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/storage_manager/storage_fs.h
Copyright: 2019-2022 Omics Data Automation Inc.
           2018-2019 Omics Data Automation Inc. and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/storage_manager/storage_gcs.h
Copyright: Google
License: Expat

Files: genomicsdb-tiledb/core/include/storage_manager/storage_hdfs.h
Copyright: 2022 Omics Data Automation Inc.
           2018 University of California, Los Angeles and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/include/storage_manager/storage_manager.h
       genomicsdb-tiledb/core/include/storage_manager/storage_manager_config.h
       genomicsdb-tiledb/core/src/array/array.cc
       genomicsdb-tiledb/core/src/array/array_iterator.cc
       genomicsdb-tiledb/core/src/array/array_schema.cc
       genomicsdb-tiledb/core/src/c_api/*
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/src/c_api/tiledb_utils.cc
Copyright: 2019-2022 Omics Data Automation Inc.
           2018-2019 Omics Data Automation Inc. and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/src/codec/*
       genomicsdb-tiledb/core/src/misc/error.cc
       genomicsdb-tiledb/core/src/storage_manager/*
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: genomicsdb-tiledb/core/src/codec/external/*
Copyright: 2011-2016 Yann Collet
License: BSD-2-clause

Files: genomicsdb-tiledb/core/src/expressions/*
       genomicsdb-tiledb/core/src/fragment/*
       genomicsdb-tiledb/core/src/fragment/book_keeping.cc
       genomicsdb-tiledb/core/src/misc/utils.cc
       genomicsdb-tiledb/core/src/storage_manager/storage_manager.cc
       genomicsdb-tiledb/core/src/storage_manager/storage_manager_config.cc
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/core/src/misc/uri.cc
       genomicsdb-tiledb/core/src/storage_manager/storage_hdfs.cc
Copyright: 2019-2022 Omics Data Automation, Inc.
           2018 University of California, Los Angeles and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/examples/*
       genomicsdb-tiledb/test/*
Copyright: 2016 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/examples/run_examples.sh
Copyright: 2019-2022 Omics Data Automation Inc.
           2018-2019 Omics Data Automation Inc. and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/examples/src/examples.h
       genomicsdb-tiledb/examples/src/tiledb_array_iterator_sparse_filter.cc
       genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_1.cc
       genomicsdb-tiledb/examples/src/tiledb_array_read_sparse_filter_2.cc
       genomicsdb-tiledb/examples/src/tiledb_delete.cc
       genomicsdb-tiledb/test/include/benchmark/*
       genomicsdb-tiledb/test/src/*
Copyright: 2018-2022 Omics Data Automation Inc.
License: Expat

Files: genomicsdb-tiledb/examples/src/tiledb_array_create_dense.cc
       genomicsdb-tiledb/examples/src/tiledb_array_create_sparse.cc
       genomicsdb-tiledb/examples/src/tiledb_ls.cc
       genomicsdb-tiledb/examples/src/tiledb_ls_workspaces.cc
       genomicsdb-tiledb/test/include/c_api/c_api_array_schema_spec.h
       genomicsdb-tiledb/test/src/c_api/*
       genomicsdb-tiledb/test/src/misc/*
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 MIT and Intel Corporation
License: Expat

Files: genomicsdb-tiledb/test/include/catch2/*
Copyright: 2020 Two Blue Cubes Ltd.
License: BSL-1.0

Files: genomicsdb-tiledb/test/include/catch2/catch.h
       genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc
       genomicsdb-tiledb/test/src/c_api/test_tiledb_utils.cc
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: scripts/*
       src/main/cpp/include/api/*
       src/main/cpp/include/query_operations/gt_remapper.h
       src/main/cpp/include/query_operations/gt_remapper_template_definition.h
       src/main/cpp/include/utils/alleles_combiner.h
       src/main/cpp/include/utils/alleles_combiner_template_definition.h
       src/main/cpp/include/utils/genomicsdb_logger.h
       src/main/cpp/include/utils/fmt_writer.h
       src/main/cpp/include/vcf/hfile_genomicsdb.h
       src/main/cpp/src/api/*
       src/main/cpp/src/config/pb_config.cc
       src/main/cpp/src/query_operations/*
       src/main/cpp/src/utils/alleles_combiner_gvcf_columnar_iterator.cc
       src/main/cpp/src/utils/genomicsdb_logger.cc
       src/main/cpp/src/vcf/*
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: src/main/cpp/include/genomicsdb/variant_array_schema.h
       src/main/cpp/include/genomicsdb/variant_storage_manager.h
       src/main/cpp/include/loader/tiledb_loader_file_base.h
       src/main/cpp/include/utils/vid_mapper.h
       src/main/cpp/src/config/json_config.cc
       src/main/cpp/src/genomicsdb/genomicsdb_iterators.cc
       src/main/cpp/src/genomicsdb/variant_array_schema.cc
       src/main/cpp/src/genomicsdb/variant_storage_manager.cc
       src/main/cpp/src/loader/load_operators.cc
       src/main/cpp/src/query_operations/broad_combined_gvcf.cc
       src/main/cpp/src/utils/known_field_info.cc
       src/main/cpp/src/utils/vid_mapper.cc
       src/main/cpp/src/vcf/vcf2binary.cc
       src/main/cpp/src/vcf/vcf_adapter.cc
       src/main/java/org/genomicsdb/reader/*
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 Intel Corporation
License: Expat

Files: src/main/cpp/include/loader/tiledb_loader_text_file.h
       src/main/cpp/src/loader/tiledb_loader_text_file.cc
Copyright: 2016-2017 Intel Corporation
License: LGPL-2

Files: src/main/cpp/src/query_operations/variant_operations.cc
       src/main/cpp/src/vcf/genomicsdb_bcf_generator.cc
       src/main/java/org/genomicsdb/reader/GenomicsDBTimer.java
Copyright: 2016-2018 Intel Corporation
License: Expat

Files: src/main/java/org/genomicsdb/GenomicsDBUtils.java
       src/main/java/org/genomicsdb/GenomicsDBUtilsJni.java
Copyright: 2019-2022 Omics Data Automation Inc.
           2018-2019 Omics Data Automation Inc. and Intel Corporation
License: Expat

Files: src/main/java/org/genomicsdb/reader/GenomicsDBQuery.java
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: src/main/java/org/genomicsdb/spark/GenomicsDBQueryInfo.java
Copyright: 2018 University of California, Los Angeles and Intel Corporation
License: Expat

Files: src/main/java/org/genomicsdb/spark/GenomicsDBSchemaFactory.java
       src/main/java/org/genomicsdb/spark/GenomicsDBVidSchema.java
       src/main/java/org/genomicsdb/spark/sources/*
       src/main/java/org/genomicsdb/spark/v2/*
Copyright: 2018-2020, Omics Data Automation
License: Expat

Files: src/main/java/org/genomicsdb/spark/sources/GenomicsDBRecordReader.java
       src/main/java/org/genomicsdb/spark/v2/GenomicsDBRecordReader.java
Copyright: 2016-2018 Intel Corporation
License: Expat

Files: src/main/jni/src/*
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 Intel Corporation
License: Expat

Files: src/main/jni/src/genomicsdb_GenomicsDBImporter.cc
Copyright: 2016-2018 Intel Corporation
License: Expat

Files: src/main/jni/src/genomicsdb_GenomicsDBQuery.cc
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: src/main/jni/src/genomicsdb_GenomicsDBUtils.cc
Copyright: 2019-2022 Omics Data Automation Inc.
           2018-2019 Omics Data Automation Inc. and Intel Corporation
License: Expat

Files: src/test/cpp/*
       src/test/java/org/genomicsdb/GenomicsDBLibLoaderTest.java
       src/test/java/org/genomicsdb/GenomicsDBUtilsTest.java
       src/test/java/org/genomicsdb/reader/*
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: src/test/cpp/include/test_mapping_data_loader.h
       src/test/cpp/src/test_mapping_data_loader.cc
       src/test/cpp/src/test_multid_vector.cc
       src/test/cpp/src/test_non_diploid_mapper.cc
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 Intel Corporation
License: Expat

Files: src/test/java/org/genomicsdb/spark/*
Copyright: 2018 University of California, Los Angeles and Intel Corporation
License: Expat

Files: tests/*
Copyright: 2018-2022 Omics Data Automation Inc.
License: Expat

Files: tests/load_genomics_metadata.sh
Copyright: 2016-2018 Intel Corporation
License: Expat

Files: tests/run.py
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 Intel Corporation
License: Expat

Files: tests/run_spark_hdfs.py
Copyright: 2019-2022 Omics Data Automation, Inc.
           2018 University of California, Los Angeles and Intel Corporation
License: Expat

Files: tools/include/common.h
       tools/src/vcf2genomicsdb_init.cc
Copyright: 2018-2022 Omics Data Automation, Inc.
License: Expat

Files: tools/src/gt_mpi_gather.cc
Copyright: 2018-2022 Omics Data Automation, Inc.
           2016-2018 Intel Corporation
License: Expat

Files: debian/*
Copyright: 2022 Pierre Gruet <pgt@debian.org>
License: Expat

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: BSD-2-clause
 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
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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:
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 this list of conditions and the following disclaimer.
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License: BSL-1.0
 Boost Software License - Version 1.0 - August 17th, 2003
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 Permission is hereby granted, free of charge, to any person or
 organization obtaining a copy of the software and accompanying
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License: FSFAP
 Copying and distribution of this file, with or without modification, are
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License: GPL-2+ with Autoconf-data exception
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License: LGPL-2
 On Debian systems the full text of the LGPL-2 can be found in
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License: Other
 You may redistribute unmodified or modified versions of this source
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License: public-domain
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