Copyright for htsjdk source package in Focal

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: 2009-2018, The Broad Institute
License: MIT

Files: debian/*
Copyright: 2010 Shaun Jackman 
           2013-2018 Olivier Sallou 
           2015 Vincent Danjean 
License: ISC
 Permission to use, copy, modify, and/or distribute this software for any
 purpose with or without fee is hereby granted, provided that the above
 copyright notice and this permission notice appear in all copies.

Files: scripts/*
  src/main/*
Copyright: 2009-2018, The Broad Institute
License: Expat

Files: src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
  src/main/java/htsjdk/samtools/BAMIteratorFilter.java
  src/main/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilter.java
  src/main/java/htsjdk/samtools/BamFileIoUtils.java
  src/main/java/htsjdk/samtools/BrowseableBAMIndex.java
  src/main/java/htsjdk/samtools/CRAMCRAIIndexer.java
  src/main/java/htsjdk/samtools/CRAMContainerStreamWriter.java
  src/main/java/htsjdk/samtools/Chunk.java
  src/main/java/htsjdk/samtools/DefaultSAMRecordFactory.java
  src/main/java/htsjdk/samtools/Defaults.java
  src/main/java/htsjdk/samtools/QueryInterval.java
  src/main/java/htsjdk/samtools/SAMRecordFactory.java
  src/main/java/htsjdk/samtools/SamFiles.java
  src/main/java/htsjdk/samtools/SamIndexes.java
  src/main/java/htsjdk/samtools/SamInputResource.java
  src/main/java/htsjdk/samtools/SamReader.java
  src/main/java/htsjdk/samtools/SamReaderFactory.java
  src/main/java/htsjdk/samtools/SamStreams.java
  src/main/java/htsjdk/samtools/SecondaryOrSupplementarySkippingIterator.java
  src/main/java/htsjdk/samtools/StreamInflatingIndexingOutputStream.java
  src/main/java/htsjdk/samtools/ValidationStringency.java
  src/main/java/htsjdk/samtools/util/AbstractAsyncWriter.java
  src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java
  src/main/java/htsjdk/samtools/util/CodeUtil.java
  src/main/java/htsjdk/samtools/util/ComparableTuple.java
  src/main/java/htsjdk/samtools/util/CoordSpanInputSteam.java
  src/main/java/htsjdk/samtools/util/DelegatingIterator.java
  src/main/java/htsjdk/samtools/util/HttpUtils.java
  src/main/java/htsjdk/samtools/util/IterableAdapter.java
  src/main/java/htsjdk/samtools/util/IterableOnceIterator.java
  src/main/java/htsjdk/samtools/util/Iterables.java
  src/main/java/htsjdk/samtools/util/Lazy.java
  src/main/java/htsjdk/samtools/util/Locatable.java
  src/main/java/htsjdk/samtools/util/LocationAware.java
  src/main/java/htsjdk/samtools/util/PositionalOutputStream.java
  src/main/java/htsjdk/samtools/util/ProgressLogger.java
  src/main/java/htsjdk/samtools/util/QualityEncodingDetector.java
  src/main/java/htsjdk/samtools/util/RelativeIso8601Date.java
  src/main/java/htsjdk/samtools/util/Tuple.java
  src/main/java/htsjdk/samtools/sra/ReferenceCache.java
  src/main/java/htsjdk/samtools/sra/SRAIndexedSequenceFile.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/main/java/htsjdk/samtools/CRAMBAIIndexer.java
Copyright: 2013, EMBL-EBI
License: Apache-2.0 or Expat

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

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
Copyright: 2015, 2016, Tim Fennell
License: Expat

Files: src/main/java/htsjdk/samtools/SAMFlag.java
Copyright: 2015 Pierre Lindenbaum
License: Expat

Files: src/main/java/htsjdk/samtools/SRAFileReader.java
  src/main/java/htsjdk/samtools/SRAIndex.java
  src/main/java/htsjdk/samtools/SRAIterator.java
  src/main/java/htsjdk/samtools/sra/*
Copyright: Public Domain
License: Public-Domain

Files: src/main/java/htsjdk/samtools/SamFlagField.java
Copyright: 2016, Nils Homer
License: Expat

Files: src/main/java/htsjdk/samtools/cram/*
Copyright: 2013, EMBL-EBI
License: Apache-2.0

Files: src/main/java/htsjdk/samtools/fastq/AsyncFastqWriter.java
  src/main/java/htsjdk/samtools/fastq/FastqWriter.java
  src/main/java/htsjdk/samtools/fastq/FastqWriterFactory.java
  src/main/java/htsjdk/samtools/filter/InsertSizeFilter.java
  src/main/java/htsjdk/samtools/filter/MappingQualityFilter.java
  src/main/java/htsjdk/samtools/filter/SecondaryAlignmentFilter.java
  src/main/java/htsjdk/samtools/filter/SecondaryOrSupplementaryFilter.java
  src/main/java/htsjdk/samtools/seekablestream/ByteArraySeekableStream.java
  src/main/java/htsjdk/samtools/seekablestream/ISeekableStreamFactory.java
  src/main/java/htsjdk/samtools/seekablestream/SeekableMemoryStream.java
  src/main/java/htsjdk/samtools/seekablestream/SeekablePathStream.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/main/java/htsjdk/samtools/filter/AbstractJavascriptFilter.java
  src/main/java/htsjdk/samtools/filter/JavascriptSamRecordFilter.java
Copyright: 2015, Pierre Lindenbaum @yokofakun Institut du Thorax - Nantes - France
License: Expat

Files: src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java
  src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java
  src/main/java/htsjdk/samtools/seekablestream/SeekableFileStream.java
Copyright: 2007-2011, The Broad Institute of MIT and Harvard.
License: LGPL-2.1

Files: src/main/java/htsjdk/samtools/util/AsyncBufferedIterator.java
Copyright: 2016, Daniel Cameron
License: Expat

Files: src/main/java/htsjdk/samtools/util/DateParser.java
Copyright: MIT, INRIA and Keio, 2000, W3C IPR SOFTWARE NOTICE / 1995-1998, World Wide Web Consortium, (Massachusetts Institute of
License: W3C-Software

Files: src/main/java/htsjdk/samtools/util/Murmur3.java
Copyright: 2011, The Guava Authors
License: Apache-2.0

Files: src/main/java/htsjdk/samtools/util/RuntimeScriptException.java
Copyright: 2009-2015, The Broad Institute
License: Expat

Files: src/main/java/htsjdk/samtools/util/TrimmingUtil.java
Copyright: 2015, 2016, Tim Fennell
License: Expat

Files: src/main/java/htsjdk/samtools/util/ftp/*
Copyright: 2007-2011, The Broad Institute of MIT and Harvard.
License: LGPL-2.1

Files: 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
Copyright: 2007-2010, The Broad Institute, Inc. and the Massachusetts Institute of Technology
License: LGPL-2.1

Files: src/main/java/htsjdk/tribble/BinaryFeatureCodec.java
Copyright: 2009-2015, The Broad Institute
License: MIT

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

Files: src/main/java/htsjdk/tribble/index/AbstractIndex.java
Copyright: 2007-2010, The Broad Institute, Inc. and the Massachusetts Institute of Technology
License: LGPL-2.1

Files: src/main/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/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: 2009-2016, The Broad Institute
License: Expat

Files: src/main/java/htsjdk/tribble/readers/AsciiLineReader.java
  src/main/java/htsjdk/tribble/readers/PositionalBufferedStream.java
Copyright: 2007-2010, The Broad Institute, Inc. and the Massachusetts Institute of Technology
License: LGPL-2.1

Files: src/main/java/htsjdk/tribble/readers/AsciiLineReaderIterator.java
  src/main/java/htsjdk/tribble/readers/LineIterator.java
  src/main/java/htsjdk/tribble/readers/LineIteratorImpl.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/main/java/htsjdk/tribble/util/*
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: 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/tribble/util/MathUtils.java
  src/main/java/htsjdk/tribble/util/ParsingUtils.java
  src/main/java/htsjdk/tribble/util/TabixUtils.java
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/main/java/htsjdk/tribble/util/popgen/*
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/main/java/htsjdk/variant/variantcontext/GenotypeJEXLContext.java
  src/main/java/htsjdk/variant/variantcontext/JEXLMap.java
  src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/main/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilter.java
Copyright: 2015, Pierre Lindenbaum @yokofakun Institut du Thorax - Nantes - France
License: Expat

Files: src/main/java/htsjdk/variant/variantcontext/writer/AsyncVariantContextWriter.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/main/java/htsjdk/variant/vcf/VCFEncoder.java
  src/main/java/htsjdk/variant/vcf/VCFFileReader.java
  src/main/java/htsjdk/variant/vcf/VCFRecordCodec.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/*
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/test/java/htsjdk/samtools/AbstractBAMFileIndexTest.java
  src/test/java/htsjdk/samtools/BAMCigarOverflowTest.java
  src/test/java/htsjdk/samtools/BAMQueryMultipleIntervalsIteratorFilterTest.java
  src/test/java/htsjdk/samtools/CRAMBAIIndexerTest.java
  src/test/java/htsjdk/samtools/CRAMCRAIIndexerTest.java
  src/test/java/htsjdk/samtools/CRAMComplianceTest.java
  src/test/java/htsjdk/samtools/CRAMContainerStreamWriterTest.java
  src/test/java/htsjdk/samtools/CRAMEdgeCasesTest.java
  src/test/java/htsjdk/samtools/CRAMFileBAIIndexTest.java
  src/test/java/htsjdk/samtools/CRAMFileCRAIIndexTest.java
  src/test/java/htsjdk/samtools/CRAMFileWriterWithIndexTest.java
  src/test/java/htsjdk/samtools/DownsamplingIteratorTests.java
  src/test/java/htsjdk/samtools/DuplicateSetIteratorTest.java
  src/test/java/htsjdk/samtools/GenomicIndexUtilTest.java
  src/test/java/htsjdk/samtools/SAMBinaryTagAndValueUnitTest.java
  src/test/java/htsjdk/samtools/SamFilesTest.java
  src/test/java/htsjdk/samtools/SamFlagFieldTest.java
  src/test/java/htsjdk/samtools/SamIndexesTest.java
  src/test/java/htsjdk/samtools/SamReaderFactoryTest.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/SAMFlagTest.java
  src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java
Copyright: 2015 Pierre Lindenbaum
License: Expat

Files: src/test/java/htsjdk/samtools/cram/*
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/cram/structure/ReadTagTest.java
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/test/java/htsjdk/samtools/fastq/*
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/filter/InsertSizeFilterTest.java
  src/test/java/htsjdk/samtools/filter/MappingQualityFilterTest.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/filter/JavascriptSamRecordFilterTest.java
Copyright: 2015, Pierre Lindenbaum @yokofakun Institut du Thorax - Nantes - France
License: Expat

Files: src/test/java/htsjdk/samtools/metrics/*
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/metrics/MetricsFileTest.java
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/test/java/htsjdk/samtools/reference/*
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/reference/FastaSequenceFileTest.java
  src/test/java/htsjdk/samtools/reference/FastaSequenceIndexTest.java
  src/test/java/htsjdk/samtools/reference/ReferenceSequenceTests.java
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/test/java/htsjdk/samtools/seekablestream/SeekableStreamFactoryTest.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/sra/*
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/util/AsyncBufferedIteratorTest.java
Copyright: 2016, Daniel Cameron
License: Expat

Files: src/test/java/htsjdk/samtools/util/CloseableIteratorTest.java
  src/test/java/htsjdk/samtools/util/CodeUtilTest.java
  src/test/java/htsjdk/samtools/util/ComparableTupleTest.java
  src/test/java/htsjdk/samtools/util/CoordSpanInputSteamTest.java
  src/test/java/htsjdk/samtools/util/HistogramTest.java
  src/test/java/htsjdk/samtools/util/OverlapDetectorTest.java
  src/test/java/htsjdk/samtools/util/QualityEncodingDetectorTest.java
  src/test/java/htsjdk/samtools/util/RelativeIso8601DateTest.java
  src/test/java/htsjdk/samtools/util/SolexaQualityConverterTest.java
  src/test/java/htsjdk/samtools/util/TupleTest.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/samtools/util/TrimmingUtilTest.java
Copyright: 2015, 2016, Tim Fennell
License: Expat

Files: src/test/java/htsjdk/tribble/bed/*
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/test/java/htsjdk/tribble/index/*
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/test/java/htsjdk/tribble/index/IndexTest.java
Copyright: 2009-2015, The Broad Institute
License: MIT

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

Files: src/test/java/htsjdk/variant/*
Copyright: 2009-2016, The Broad Institute
License: Expat

Files: src/test/java/htsjdk/variant/variantcontext/VariantContextBuilderTest.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/variant/variantcontext/filter/CompoundFilterTest.java
  src/test/java/htsjdk/variant/variantcontext/filter/PassingVariantFilterTest.java
  src/test/java/htsjdk/variant/variantcontext/filter/SnpFilterTest.java
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/variant/variantcontext/filter/JavascriptVariantFilterTest.java
Copyright: 2015, Pierre Lindenbaum @yokofakun Institut du Thorax - Nantes - France
License: Expat

Files: src/test/java/htsjdk/variant/vcf/*
Copyright: 2009-2015, The Broad Institute
License: MIT

Files: src/test/java/htsjdk/variant/vcf/IndexFactoryUnitTest.java
  src/test/java/htsjdk/variant/vcf/VCFCompoundHeaderLineUnitTest.java
  src/test/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java
  src/test/java/htsjdk/variant/vcf/VCFStandardHeaderLinesUnitTest.java
Copyright: 2009-2016, The Broad Institute
License: Expat

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
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 Unless required by applicable law or agreed to in writing, software
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 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
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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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