Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: https://github.com/samtools/htsjdk/releases
Comment: Convenience binary jar files are removed.
Files-Excluded: gradle/wrapper/gradle-wrapper.jar

Files: *
Copyright: 2009-2020 The Broad Institute
License: Expat

Files: src/main/java/htsjdk/samtools/CRAMFileReader.java
       src/main/java/htsjdk/samtools/CRAMFileWriter.java
       src/main/java/htsjdk/samtools/CRAMIterator.java
       src/main/java/htsjdk/samtools/cram/*
Copyright: 2013-2016 EMBL-EBI
License: Apache-2.0

Files: src/main/java/htsjdk/samtools/CRAMBAIIndexer.java
Copyright: 2013-2016 EMBL-EBI
           2014 The Broad Institute
License: Apache-2.0 and Expat
Comment:
 The file carries both notices: the EMBL-EBI Apache-2.0 header and the
 Broad Institute MIT licence.

Files: src/main/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.java
Copyright: 2004-2009 The Broad Institute
           2003 Jan Wigginton, Goncalo Abecasis
License: Expat
Comment:
 hwCalculate() is credited to Wigginton and Abecasis (2003), the authors
 of the exact SNP-HWE test; the file is distributed by the Broad Institute
 under the MIT licence.

Files: gradlew
       gradlew.bat
Copyright: 2015-2021 the original authors
License: Apache-2.0
Comment: The Gradle wrapper scripts (the wrapper jar is excluded).

Files: src/test/resources/htsjdk/hts-specs/*
Copyright: 2019-2023 Genome Research Ltd.
           2021 John Marshall
           EBI (European Bioinformatics Institute)
           2022-2024 Daniel Cameron
License: Apache-2.0
Comment:
 Test data from the GA4GH hts-specs test suite; the LICENSE file of each
 subdirectory gives the holders and the Apache-2.0 licence. The vcf
 LICENSE notes that complexfile_passed_000.vcf looks like a subset of 1000
 Genomes data, which may instead be under the 1000 Genomes terms (freely
 available, Fort Lauderdale Agreement).

Files: src/test/resources/htsjdk/hts-specs/test/cram/codecs/*
Copyright: 2019-2023 Genome Research Ltd.
License: Apache-2.0 or BSD-3-clause
Comment:
 "jointly available under the Apache 2.0 license and the BSD license"
 (from Staden io_lib and htscodecs).

Files: src/test/resources/htsjdk/hts-specs/test/SAMtags/parse_mm.pl
Copyright: 2020 Genome Research Ltd.
License: BSD-3-clause

Files: src/test/resources/htsjdk/hts-specs/test/sam/compare_sam.pl
Copyright: 2013-2018 Genome Research Ltd.
License: Expat

Files: src/main/java/htsjdk/samtools/ChainedDownsamplingIterator.java
       src/main/java/htsjdk/samtools/ConstantMemoryDownsamplingIterator.java
       src/main/java/htsjdk/samtools/DownsamplingIteratorFactory.java
       src/main/java/htsjdk/samtools/HighAccuracyDownsamplingIterator.java
       src/main/java/htsjdk/samtools/SAMRecordQueryHashComparator.java
       src/main/java/htsjdk/samtools/util/TrimmingUtil.java
       src/test/java/htsjdk/samtools/util/TrimmingUtilTest.java
Copyright: 2015-2016 Tim Fennell
License: Expat

Files: src/main/java/htsjdk/samtools/SAMFlag.java
       src/main/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java
       src/main/java/htsjdk/samtools/filter/JavascriptSamRecordFilter.java
       src/main/java/htsjdk/samtools/util/RuntimeScriptException.java
       src/main/java/htsjdk/variant/variantcontext/StructuralVariantType.java
       src/main/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java
       src/test/java/htsjdk/samtools/SAMFlagTest.java
       src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java
       src/test/java/htsjdk/samtools/filter/JavascriptSamRecordFilterTest.java
       src/test/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java
Copyright: Pierre Lindenbaum PhD @yokofakun Institut du Thorax - Nantes - France
License: Expat

Files: src/main/java/htsjdk/samtools/SamFlagField.java
       src/main/java/htsjdk/samtools/util/IntervalCodec.java
       src/main/java/htsjdk/samtools/util/IntervalCoordinateComparator.java
       src/test/java/htsjdk/samtools/SAMFileHeaderTest.java
       src/test/java/htsjdk/samtools/util/IntervalCodecTest.java
Copyright: 2016-2019 Nils Homer
License: Expat

Files: src/main/java/htsjdk/samtools/cram/BAIEntry.java
       src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java
       src/main/java/htsjdk/samtools/cram/build/SliceFactory.java
       src/main/java/htsjdk/samtools/cram/compression/*
       src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanCanoncialCodeGenerator.java
       src/main/java/htsjdk/samtools/cram/encoding/core/huffmanUtils/HuffmanParams.java
       src/main/java/htsjdk/samtools/cram/ref/CRAMLazyReferenceSource.java
       src/main/java/htsjdk/samtools/cram/structure/AlignmentContext.java
       src/main/java/htsjdk/samtools/cram/structure/CRAMCompressionRecord.java
       src/main/java/htsjdk/samtools/cram/structure/CRAMEncodingStrategy.java
       src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java
       src/main/java/htsjdk/samtools/cram/structure/CompressionHeaderEncodingMap.java
       src/main/java/htsjdk/samtools/cram/structure/CompressorCache.java
       src/main/java/htsjdk/samtools/cram/structure/ContainerHeader.java
       src/main/java/htsjdk/samtools/cram/structure/SliceBlocks.java
       src/main/java/htsjdk/samtools/cram/structure/SliceBlocksReadStreams.java
       src/main/java/htsjdk/samtools/cram/structure/SliceBlocksWriteStreams.java
Copyright: 2009-2020 The Broad Institute
License: Expat

Files: src/main/java/htsjdk/samtools/fastq/FastqEncoder.java
       src/main/java/htsjdk/samtools/reference/AbstractIndexedFastaSequenceFile.java
       src/main/java/htsjdk/samtools/reference/BlockCompressedIndexedFastaSequenceFile.java
       src/main/java/htsjdk/samtools/reference/FastaSequenceIndexCreator.java
       src/main/java/htsjdk/samtools/util/GZIIndex.java
       src/test/java/htsjdk/samtools/CigarOperatorUnitTest.java
       src/test/java/htsjdk/samtools/SAMRecordQueryHashComparatorTest.java
       src/test/java/htsjdk/samtools/SAMRecordQueryNameComparatorTest.java
       src/test/java/htsjdk/samtools/fastq/*
       src/test/java/htsjdk/samtools/reference/FastaSequenceIndexCreatorTest.java
       src/test/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java
       src/test/java/htsjdk/samtools/seekablestream/SeekableStreamTest.java
       src/test/java/htsjdk/samtools/util/BufferedLineReaderTest.java
       src/test/java/htsjdk/samtools/util/GZIIndexTest.java
       src/test/java/htsjdk/samtools/util/PositionalOutputStreamTest.java
Copyright: 2015-2018 Daniel Gomez-Sanchez
License: Expat

Files: src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java
       src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java
       src/main/java/htsjdk/samtools/util/ftp/*
       src/main/java/htsjdk/tribble/util/HTTPHelper.java
       src/main/java/htsjdk/tribble/util/URLHelper.java
Copyright: 2007-2011 The Broad Institute of MIT and Harvard.
License: LGPL-2.1

Files: src/main/java/htsjdk/samtools/seekablestream/SeekableFileStream.java
       src/main/java/htsjdk/tribble/AbstractFeatureReader.java
       src/main/java/htsjdk/tribble/AsciiFeatureCodec.java
       src/main/java/htsjdk/tribble/FeatureCodec.java
       src/main/java/htsjdk/tribble/FeatureReader.java
       src/main/java/htsjdk/tribble/index/AbstractIndex.java
       src/main/java/htsjdk/tribble/index/interval/*
       src/main/java/htsjdk/tribble/readers/AsciiLineReader.java
       src/main/java/htsjdk/tribble/readers/PositionalBufferedStream.java
       src/test/java/htsjdk/tribble/index/interval/*
Copyright: 2007-2010 The Broad Institute, Inc. and the Massachusetts Institute of Technology.
License: LGPL-2.1

Files: src/main/java/htsjdk/samtools/util/AsyncBlockCompressedInputStream.java
       src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java
       src/test/java/htsjdk/samtools/util/AsyncBlockCompressedInputStreamTest.java
       src/test/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java
Copyright: 2016 Daniel Cameron
License: Expat

Files: src/main/java/htsjdk/samtools/util/DateParser.java
       src/test/java/htsjdk/samtools/util/DateParserTest.java
Copyright: 2000 MIT, INRIA and Keio
           1995-1998 World Wide Web Consortium, (Massachusetts Institute of Technology, Institut National de Recherche en Informatique et en Automatique, Keio University)
License: W3C-Software

Files: src/main/java/htsjdk/samtools/util/Murmur3.java
Copyright: 2011 The Guava Authors
           Austin Appleby
License: Apache-2.0 and Public-Domain

Files: src/main/java/htsjdk/tribble/CloseableTribbleIterator.java
       src/main/java/htsjdk/tribble/index/linear/*
       src/test/java/htsjdk/tribble/index/linear/*
Copyright: 2009-2010 The Broad Institute, Inc.
License: LGPL-2.1

Files: src/main/java/htsjdk/tribble/index/linear/LinearIndexCreator.java
Copyright: 2009-2020 The Broad Institute
License: Expat

Files: src/main/java/htsjdk/variant/utils/BinomialCoefficientUtil.java
Copyright: 2001-2016 The Apache Software Foundation
           2010-2012 CS Systèmes dInformation
License: Apache-2.0

Files: src/test/java/htsjdk/samtools/util/AsyncWriterTest.java
Copyright: 2016 Len Trigg
License: Expat

Files: debian/*
Copyright: 2010 Shaun Jackman <sjackman@debian.org>
           2013-2018 Olivier Sallou <osallou@debian.org>
           2015 Vincent Danjean <vdanjean@debian.org>
License: ISC

Files: debian/tests/beagle-run-sample-analysis
       debian/tests/chromhmm-run-sample-analysis
Copyright: 2016-2021 Dylan Aïssi <daissi@debian.org>
License: Expat
Comment: These files come from the packages beagle and chromhmm, licenses were
 changed from GPL-3+ to Expat after discussion with the copyright holder.

Files: debian/tests/drop-seq-run-unit-test
       debian/tests/pilon-run-unit-test
Copyright: 2020 Andreas Tille <tille@debian.org>
License: Expat

Files: debian/tests/fastqc-run-unit-test
Copyright: 2012 Steffen Moeller <moeller@debian.org>
License: Expat
Comment: This file comes from the package fastqc, the license was changed from
 GPL-3+ to Expat after discussion with the copyright holder.

Files: debian/tests/jalview-run-unit-test
Copyright: 2020-2021 Pierre Gruet <pgt@debian.org>
License: Expat

Files: debian/tests/picard-tools-run-unit-test
Copyright: 2010 Shaun Jackman <sjackman@debian.org>
           2013-2018 Olivier Sallou <osallou@debian.org>
           2015-2016 Vincent Danjean <vdanjean@debian.org>
           2016-2018 Andreas Tille <tille@debian.org>
License: ISC

License: Apache-2.0
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
 .
     http://www.apache.org/licenses/LICENSE-2.0
 .
 Unless required by applicable law or agreed to in writing, software
 distributed under the License is distributed on an "AS IS" BASIS,
 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 See the License for the specific language governing permissions and
 limitations under the License.
Comment: On Debian systems, the complete text of the Apache License version 2.0
 is available in the file ‘/usr/share/common-licenses/Apache-2.0’.

License: Expat
 The MIT License
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 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
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License: LGPL-2.1
 Quoted from ‘/usr/share/common-licenses/LGPL-2.1’:
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 This library is free software; you can redistribute it and/or
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License: ISC
 Permission to use, copy, modify, and/or distribute this software for any
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