[med-svn] [htsjdk] 04/11: Rewrote copyright and remove convenience jar file for gradle
Vincent Danjean
vdanjean at debian.org
Wed Jul 6 23:05:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a commit to branch master
in repository htsjdk.
commit b205f832ab1c5271c5f71822a66bd5ba37384504
Author: Vincent Danjean <Vincent.Danjean at ens-lyon.org>
Date: Wed Jul 6 23:21:40 2016 +0200
Rewrote copyright and remove convenience jar file for gradle
---
debian/changelog | 5 +-
debian/copyright | 579 ++++++++++++++++++++++++++++++++++++++++++-------------
2 files changed, 447 insertions(+), 137 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index a995e28..295342e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-htsjdk (2.5.0+dfsg-1) UNRELEASED; urgency=medium
+htsjdk (2.5.0+dfsg.2-1) UNRELEASED; urgency=medium
[ Andreas Tille ]
* New upstream version
@@ -9,8 +9,9 @@ htsjdk (2.5.0+dfsg-1) UNRELEASED; urgency=medium
[ Vincent Danjean ]
* Skip tests checking the use of the local zip implementation
* Adaptation to the new gradle build system
+ * Rework debian/copyright (new source layout)
- -- Andreas Tille <tille at debian.org> Fri, 20 May 2016 11:37:24 +0200
+ -- Vincent Danjean <vdanjean at debian.org> Wed, 06 Jul 2016 23:19:17 +0200
htsjdk (2.1.1+dfsg.1-1) unstable; urgency=medium
diff --git a/debian/copyright b/debian/copyright
index e57981e..4bb3923 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -7,79 +7,448 @@ Files: *
Copyright: 2009-2015, The Broad Institute
License: MIT
-Files:
- src/main/java/htsjdk/samtools/SAMFlag.java
- src/test/java/htsjdk/samtools/SAMFlagTest.java
- src/test/java/htsjdk/samtools/SAMSequenceDictionaryTest.java
-Copyright: 2015 Pierre Lindenbaum
+Files: debian/*
+Copyright: 2010 Shaun Jackman <sjackman at debian.org>
+ 2013 Olivier Sallou <osallou at debian.org>
+ 2015 Vincent Danjean <vdanjean at 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: debian/copyright2
+Copyright: 2013, EMBL-EBI
+ 2009-2016, The Broad Institute
License: MIT
-Files: src/main/java/htsjdk/tribble/util/popgen/HardyWeinbergCalculation.java
-Copyright:
- 2003, Jan Wigginton, Goncalo Abecasis (goncalo at umich.edu)
- 2004, 2009, The Broad Institute
+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/SAMFileTruncatedReader.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/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/util/DateParser.java
-Copyright: 2000 MIT, INRIA and Keio
-License: W3C-Software
+Files: src/main/java/htsjdk/samtools/CRAMBAIIndexer.java
+Copyright: 2013, EMBL-EBI
+License: Apache-2.0 or Expat
-Files: etc/test/junit-noframes.xsl
-Copyright: 2001-2004, The Apache Software Foundation
+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/c/inteldeflater/IntelDeflater.c
- src/main/java/htsjdk/samtools/util/zip/IntelDeflater.java
- src/main/java/htsjdk/samtools/util/zip/ZStreamRef.java
-Copyright: (c) 1996, 1996, 2009, 2010, Oracle and/or its affiliates. All rights reserved.
-License: GPL-2 with Classpath exception
+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/*
+License: Public-Domain
-Files:
- src/main/java/htsjdk/samtools/CRAM*.java
- src/main/java/htsjdk/samtools/cram/*
+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/seekablestream/SeekableFileStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStream.java
- src/main/java/htsjdk/samtools/seekablestream/SeekableFTPStreamHelper.java
- src/main/java/htsjdk/samtools/util/ftp/FTPClient.java
- src/main/java/htsjdk/samtools/util/ftp/FTPReply.java
- src/main/java/htsjdk/samtools/util/ftp/FTPStream.java
- src/main/java/htsjdk/samtools/util/ftp/FTPUtils.java
- src/main/java/htsjdk/tribble/AbstractFeatureReader.java
- src/main/java/htsjdk/tribble/AsciiFeatureCodec.java
- src/main/java/htsjdk/tribble/CloseableTribbleIterator.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/Interval.java
- src/main/java/htsjdk/tribble/index/interval/IntervalIndexCreator.java
- src/main/java/htsjdk/tribble/index/interval/IntervalTree.java
- src/main/java/htsjdk/tribble/index/interval/IntervalTreeIndex.java
- src/main/java/htsjdk/tribble/index/linear/LinearIndex.java
- src/main/java/htsjdk/tribble/readers/AsciiLineReader.java
- src/main/java/htsjdk/tribble/readers/PositionalBufferedStream.java
- src/main/java/htsjdk/tribble/util/HTTPHelper.java
- src/main/java/htsjdk/tribble/util/URLHelper.java
- src/test/java/htsjdk/tribble/index/linear/LinearIndexTest.java
- src/test/java/htsjdk/tribble/index/interval/IntervalTreeTest.java
-Copyright:
- 2007-2010, The Broad Institute, Inc. and the Massachusetts Institute of Technology
- 2007-2011, The Broad Institute of MIT and Harvard.
- 2009-2010, The Broad Institute, Inc
+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: debian/*
-Copyright: 2010 Shaun Jackman <sjackman at debian.org>
- 2013 Olivier Sallou <osallou at debian.org>
- 2015 Vincent Danjean <vdanjean at 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: 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.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ 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
+ .
+ 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
+ use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to
+ whom the Software is furnished to do so, subject to the
+ following conditions:
+ .
+ The above copyright notice and this permission notice shall
+ be included in all copies or substantial portions of the
+ Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT
+ WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+ INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR
+ PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+ SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+License: LGPL-2.1
+ Quoted from ‘/usr/share/common-licenses/LGPL-2.1’:
+ .
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+ .
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
License: MIT
Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -151,80 +520,20 @@ License: W3C-Software
permission. Title to copyright in this software and any associated
documentation will at all times remain with copyright holders.
-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
+License: Public-Domain
+ This software/database is a "United States Government Work" under the
+ terms of the United States Copyright Act. It was written as part of
+ the author's official duties as a United States Government employee and
+ thus cannot be copyrighted. This software/database is freely available
+ to the public for use. The National Library of Medicine and the U.S.
+ Government have not placed any restriction on its use or reproduction.
.
- http://www.apache.org/licenses/LICENSE-2.0
+ Although all reasonable efforts have been taken to ensure the accuracy
+ and reliability of the software and data, the NLM and the U.S.
+ Government do not and cannot warrant the performance or results that
+ may be obtained by using this software or data. The NLM and the U.S.
+ Government disclaim all warranties, express or implied, including
+ warranties of performance, merchantability or fitness for any particular
+ purpose.
.
- 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: GPL-2 with Classpath exception
- This code is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License version 2 only, as
- published by the Free Software Foundation. Oracle designates this
- particular file as subject to the "Classpath" exception as provided
- by Oracle in the LICENSE file that accompanied this code.
- .
- This code is distributed in the hope that it will be useful, but WITHOUT
- ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- version 2 for more details (a copy is included in the LICENSE file that
- accompanied this code).
- .
- You should have received a copy of the GNU General Public License version
- 2 along with this work; if not, write to the Free Software Foundation,
- Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- .
- Please contact Oracle, 500 Oracle Parkway, Redwood Shores, CA 94065 USA
- or visit www.oracle.com if you need additional information or have any
- questions.
-Comment:
- Comment on Classpath exception: here is quote from
- http://spdx.org/licenses/GPL-2.0-with-classpath-exception
- .
- Linking this library statically or dynamically with other modules is making a
- combined work based on this library. Thus, the terms and conditions of the GNU
- General Public License cover the whole combination.
- .
- As a special exception, the copyright holders of this library give you
- permission to link this library with independent modules to produce an
- executable, regardless of the license terms of these independent modules, and
- to copy and distribute the resulting executable under terms of your choice,
- provided that you also meet, for each linked independent module, the terms and
- conditions of the license of that module. An independent module is a module
- which is not derived from or based on this library. If you modify this library,
- you may extend this exception to your version of the library, but you are not
- obligated to do so. If you do not wish to do so, delete this exception
- statement from your version
- .
- .
- Comment on the GPL-2:
- .
- On Debian systems, the complete text of the GNU General Public License
- version 2 is available in the file ‘/usr/share/common-licenses/GPL-2’.
-
-License: LGPL-2.1
- Quoted from ‘/usr/share/common-licenses/LGPL-2.1’:
- .
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Lesser General Public
- License as published by the Free Software Foundation; either
- version 2.1 of the License, or (at your option) any later version.
- .
- This library is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- Lesser General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-
+ Please cite the author in any work or product based on this material.
--
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