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 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 License: Expat Files: genomicsdb-htslib/htslib/kfunc.h genomicsdb-htslib/kfunc.c Copyright: 2011 Attractive Chaos 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 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 2004 Scott James Remnant . 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 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 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. 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