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 <sjackman@debian.org>
2013-2018 Olivier Sallou <osallou@debian.org>
2015 Vincent Danjean <vdanjean@debian.org>
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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See the License for the specific language governing permissions and
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Comment: On Debian systems, the complete text of the Apache License version 2.0
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License: Expat
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