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 2013-2018 Olivier Sallou 2015 Vincent Danjean License: ISC Files: debian/tests/beagle-run-sample-analysis debian/tests/chromhmm-run-sample-analysis Copyright: 2016-2021 Dylan Aïssi 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. 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