Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Goby Upstream-Contact: goby-framework@googlegroups.com Source: https://github.com/CampagneLaboratory/goby3/releases Files-Excluded: */*.jar goby-distribution/data models testsupport/*/lib test-data/bam/Example.bam test-data/bam/Example-sorted.bam test-data/bam/Example2.bam test-data/seq-var-test/seq-var-reads-gsnap.html Comment: We remove jar files that are bundled with the source. Also we remove a html file with very long lines that is unused. Finally, we remove very large test data files. Some tests must be deactivated, but they were succeeding before. Files: * Copyright: 2009-2017 Institute for Computational Biomedicine License: GPL-3+ Files: cpp/* Copyright: 2009 Peter Adolphs 2008 Thomas Porschberg License: FSFAP Files: cpp/m4/ax_boost_date_time.m4 Copyright: 2008 Thomas Porschberg 2008 Michael Tindal License: FSFAP Files: cpp/m4/ax_boost_filesystem.m4 Copyright: 2009 Thomas Porschberg 2009 Roman Rybalko 2009 Michael Tindal License: FSFAP Files: cpp/m4/ax_boost_program_options.m4 Copyright: 2009 Thomas Porschberg License: FSFAP Files: cpp/m4/ax_boost_system.m4 Copyright: 2008 Thomas Porschberg 2008 Michael Tindal 2008 Daniel Casimiro License: FSFAP Files: cpp/src/* Copyright: 2009-2012 Institute for Computational Biomedicine License: LGPL-3+ Files: cpp/src/Makefile.am Copyright: 2009-2017 Institute for Computational Biomedicine License: GPL-3+ Files: cpp/src/goby/ICBFileInputStream.cc cpp/src/goby/ICBFileInputStream.h Copyright: 2008 Google Inc. License: BSD-3-clause Files: cpp/src/kseq.h Copyright: 2008 Genome Research Ltd (GRL). License: Expat Files: goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java Copyright: 2002-2011 Sebastiano Vigna 2009-2012 Institute for Computational Biomedicine License: LGPL-3+ and GPL-3+ Files: goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java Copyright: 2002-2011 Sebastiano Vigna 2012 Fabien Campagne License: LGPL-3+ Files: goby-distribution/src/main/java/org/campagnelab/goby/GobyVersion.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AbstractAlignmentReader.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignedSequence.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentPositionComparator.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReaderImpl.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentStats.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentWriterImpl.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/IterateAlignments.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/IterateSortedAlignments.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/LastParser.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/Merge.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/ScanReferenceSequence.java goby-distribution/src/main/java/org/campagnelab/goby/alignments/filters/* goby-distribution/src/main/java/org/campagnelab/goby/baseinfo/* goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java goby-distribution/src/main/java/org/campagnelab/goby/counts/* goby-distribution/src/main/java/org/campagnelab/goby/exception/* goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractGobyMode.java goby-distribution/src/main/java/org/campagnelab/goby/modes/ColorSpaceConverter.java goby-distribution/src/main/java/org/campagnelab/goby/modes/GenericToolsDriver.java goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java goby-distribution/src/main/java/org/campagnelab/goby/modes/UpgradeMode.java goby-distribution/src/main/java/org/campagnelab/goby/modes/core/* goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.java goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.java goby-distribution/src/main/java/org/campagnelab/goby/readers/* goby-distribution/src/main/java/org/campagnelab/goby/reads/CompressedRead.java goby-distribution/src/main/java/org/campagnelab/goby/reads/MultiReads.java goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java goby-distribution/src/main/java/org/campagnelab/goby/reads/RandomAccessSequenceCache.java goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadSet.java goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsLoader.java goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsReader.java goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsWriterImpl.java goby-distribution/src/main/java/org/campagnelab/goby/reads/SequenceDigests.java goby-distribution/src/main/java/org/campagnelab/goby/reads/SequenceEncoder.java goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestPositionSlices.java Copyright: 2009-2012 Institute for Computational Biomedicine License: LGPL-3+ Files: goby-distribution/src/main/java/org/campagnelab/goby/counts/CachingCountsArchiveReader.java goby-distribution/src/main/java/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.java goby-distribution/src/main/java/org/campagnelab/goby/counts/CountBinningAdapterI.java goby-distribution/src/main/java/org/campagnelab/goby/counts/CountBinningAdaptor.java goby-distribution/src/main/java/org/campagnelab/goby/counts/CountIndexBuilder.java goby-distribution/src/main/java/org/campagnelab/goby/counts/CountWriterHelper2.java goby-distribution/src/main/java/org/campagnelab/goby/counts/CountsAggregatorI.java goby-distribution/src/main/java/org/campagnelab/goby/counts/CountsWriterI.java goby-distribution/src/main/java/org/campagnelab/goby/counts/PositionAdapter.java goby-distribution/src/main/java/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.java goby-distribution/src/main/java/org/campagnelab/goby/counts/UnionDumpIterator.java goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/* goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/GroupAssociations.java Copyright: 2009-2017 Institute for Computational Biomedicine License: GPL-3+ Files: debian/* Copyright: 2012 Andreas Tille 2020-2021 Pierre Gruet License: LGPL-3+ License: GPL-3+ On Debian systems the full text of the GPL-3 can be found in /usr/share/common-licenses/GPL-3 License: FSFAP Copying and distribution of this file, with or without modification, are permitted in any medium without royalty provided the copyright notice and this notice are preserved. This file is offered as-is, without any warranty. License: LGPL-3+ On Debian systems the full text of the LGPL-3 can be found in /usr/share/common-licenses/LGPL-3 License: BSD-3-clause Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, and the entire permission notice in its entirety, including the disclaimer of warranties. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. . THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. License: Expat 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.