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
License: Apache-2.0 or 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: 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: 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
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 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: W3C-Software
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 Copyright 1995-1998 World Wide Web Consortium, (Massachusetts Institute of
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