Format: http://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: 2009-2015, The Broad Institute License: MIT Files: debian/* Copyright: 2010 Shaun Jackman 2013 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: 2009-2016, 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 src/main/java/htsjdk/tribble/readers/LineReaderUtil.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/fastq/FastqWriterTest.java Copyright: 2009-2015, The Broad Institute License: Expat 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/IndexedFastaSequenceFileTest.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. 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