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 <thomas@randspringer.de>
License: FSFAP

Files: cpp/m4/ax_boost_date_time.m4
Copyright: 2008 Thomas Porschberg <thomas@randspringer.de>
           2008 Michael Tindal
License: FSFAP

Files: cpp/m4/ax_boost_filesystem.m4
Copyright: 2009 Thomas Porschberg <thomas@randspringer.de>
           2009 Roman Rybalko <libtorrent@romanr.info>
           2009 Michael Tindal
License: FSFAP

Files: cpp/m4/ax_boost_program_options.m4
Copyright: 2009 Thomas Porschberg <thomas@randspringer.de>
License: FSFAP

Files: cpp/m4/ax_boost_system.m4
Copyright: 2008 Thomas Porschberg <thomas@randspringer.de>
           2008 Michael Tindal
           2008 Daniel Casimiro <dan.casimiro@gmail.com>
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 <tille@debian.org>
           2020-2021 Pierre Gruet <pgt@debian.org>
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.
