Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://www.broadinstitute.org/igv/projects/downloads
Files-Excluded:
    lib/batik*
    lib/commons*
    lib/guava*
    */htsjdk*.jar
    lib/jcommon*
    lib/jfreechart*
    */junit-*.jar
    lib/log4j-*
    */picard-*.jar
    */snappy-java-*.jar
    lib/swing-layout-*
    lib/jide-oss-*
    lib/gson*
    */ant.jar
    */fest-Assert*.jar
    test/lib/fest-util*.jar
    test/lib/fest-reflect*.jar
Disclaimer: This package is not part of the Debian operating system.
 The igv source and binary Debian packages are part of the “non-free” area in
 our archive. The packages in this area are not part of the Debian system,
 although they have been configured for use with Debian. We nevertheless support
 the use of the igv source and binary Debian packages and provide infrastructure
 for non-free packages (such as our bug tracking system and mailing lists).

Files: *
Copyright: 2007-2018 Broad Institute
License: Expat

Files: lib/goby-io-igv*.jar
Copyright: 2012-2014 Campagne Laboratory, Weill Cornell Medical College
License: LGPL-3

Files: src/main/java/biz/*
Copyright: 2003-2010 Christian dHeureuse, Inventec Informatik AG, Zurich, Switzerland
License: Expat

Files: src/main/java/com/*
Copyright: 2010-2012 penSec.IT UG
           2005      Ewan Mellor
           2002      Vidar Holen
           2002      Michal Ceresna
           2001-2012 Steve Purcell
License: BSD-3-clause

Files: src/main/java/org/apache/*
Copyright: 1999      The Apache Software Foundation
License: Apache-1.1

Files: src/main/java/org/broad/igv/event/GenomeChangeEvent.java
       src/main/java/org/broad/igv/event/IGVEventBus.java
       src/main/java/org/broad/igv/event/IGVEventObserver.java
       src/main/java/org/broad/igv/event/ReferenceFrameEvent.java
       src/main/java/org/broad/igv/feature/basepair/*
       src/main/java/org/broad/igv/feature/bionano/*
       src/main/java/org/broad/igv/feature/genome/SequenceInterval.java
       src/main/java/org/broad/igv/maf/MAFtoSAM.java
       src/main/java/org/broad/igv/sam/InsertionManager.java
       src/main/java/org/broad/igv/sam/InsertionSelectionEvent.java
       src/main/java/org/broad/igv/sam/ReadStats.java
       src/main/java/org/broad/igv/sam/cram/*
       src/main/java/org/broad/igv/tools/RepeatMaskSplitter.java
       src/main/java/org/broad/igv/tools/PairedUtils.java
       src/main/java/org/broad/igv/tools/sort/BAMSorter.java
       src/main/java/org/broad/igv/tools/sort/Sorter.java
       src/main/java/org/broad/igv/tools/sort/SorterFactory.java
       src/main/java/org/broad/igv/track/Range.java
       src/main/java/org/broad/igv/track/ScalableTrack.java
       src/main/java/org/broad/igv/ui/util/ByteSubArray.java
       src/main/java/org/broad/igv/util/IntervalTree.java
       src/main/java/org/broad/igv/util/TutorialUtils.java
       src/test/java/org/broad/igv/sam/cram/CRAMReaderTest.java
Copyright: 2015-2016 University of California San Diego
License: Expat

Files: src/main/java/org/broad/igv/feature/SpliceJunctionFeature.java
       src/main/java/org/broad/igv/sam/SpliceJunctionHelper.java
       src/main/java/org/broad/igv/sam/SpliceJunctionTrack.java
Copyright: 2007-2015 Fred Hutchinson Cancer Research Center and Broad Institute
License: Expat

Files: src/main/java/org/broad/igv/goby/*
       src/test/java/org/broad/igv/goby/*
Copyright: 2007-2015 Institute for Computational Biomedicine
License: Expat

Files: src/main/java/org/broad/igv/renderer/SpliceJunctionRenderer.java
Copyright: 2013      F. Hoffmann-La Roche Ltd and Tessella Inc.
           2007-2015 Fred Hutchinson Cancer Research Center and Broad Institute
License: Expat

Files: src/main/java/org/broad/igv/track/PackedFeaturesSpliceJunctions.java
       src/main/java/org/broad/igv/ui/panel/RegionNavigatorDialog.java
       src/main/java/org/broad/igv/util/ObservableForObject.java
Copyright: 2007-2015 Fred Hutchinson Cancer Research Center and Broad Institute
License: Expat

Files: src/main/java8/apple/dts/samplecode/osxadapter/OSXAdapter.java
Copyright: 2003-2007 Apple, Inc.
License: AML

Files: web/*
Copyright: 2007, Memorial Sloan-Kettering Cancer Center.
License: LGPL-2.1

Files: src/main/resources-jlfgr-1_0/*
Copyright: 2000 by Sun Microsystems, Inc.
License: other
 Sun grants you ("Licensee") a non-exclusive,
 royalty free, license to use, and redistribute
 this software graphics artwork, as individual
 graphics or as a collection, as part of software
 code or programs that you develop, provided that
 i) this copyright notice and license accompany
 the software graphics artwork; and ii) you do not
 utilize the software graphics artwork in a manner
 which is disparaging to Sun. Unless enforcement
 is prohibited by applicable law, you may not
 modify the graphics, and must use them true to
 color and unmodified in every way.
 .
 This software graphics artwork is provided "AS
 IS," without a warranty of any kind. ALL EXPRESS
 OR IMPLIED CONDITIONS, REPRESENTATIONS AND
 WARRANTIES, INCLUDING ANY IMPLIED WARRANTY OF
 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE
 OR NON-INFRINGEMENT, ARE HEREBY EXCLUDED. SUN AND
 ITS LICENSORS SHALL NOT BE LIABLE FOR ANY DAMAGES
 SUFFERED BY LICENSEE AS A RESULT OF USING,
 MODIFYING OR DISTRIBUTING THE SOFTWARE GRAPHICS
 ARTWORK.
 .
 IN NO EVENT WILL SUN OR ITS LICENSORS BE LIABLE
 FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR
 DIRECT, INDIRECT, SPECIAL, CONSEQUENTIAL,
 INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED
 AND REGARDLESS OF THE THEORY OF LIABILITY,
 ARISING OUT OF THE USE OF OR INABILITY TO USE
 SOFTWARE GRAPHICS ARTWORK, EVEN IF SUN HAS BEEN
 ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
 .
 If any of the above provisions are held to be in
 violation of applicable law, void, or
 unenforceable in any jurisdiction, then such
 provisions are waived to the extent necessary for
 this Disclaimer to be otherwise enforceable in
 such jurisdiction.

Files: debian/*
Copyright: 2010-2011 Shaun Jackman <sjackman@debian.org>
           2011      Charles Plessy <plessy@debian.org>
           2013-2018 Olivier Sallou <osallou@debian.org>,
                     Andreas Tille <tille@debian.org>
           2020      Pierre Gruet <pgtdebian@free.fr>
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.

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.

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:
 Redistributions of source code must retain the above copyright notice, this
 list of conditions and the following disclaimer. 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. Neither the name of the copyright holder nor the names
 of its contributors may be used to endorse or promote products derived from
 this software without specific prior written permission.
 .
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 COPYRIGHT HOLDERS OR CONTRIBUTORS 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: Apache-1.1
 The Apache Software License, Version 1.1
 .
 Copyright (c) 2000 The Apache Software Foundation.  All rights
 reserved.
 .
 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, this list of conditions and the following disclaimer.
 .
 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 end-user documentation included with the redistribution,
    if any, must include the following acknowledgment:
       "This product includes software developed by the
        Apache Software Foundation (http://www.apache.org/)."
    Alternately, this acknowledgment may appear in the software itself,
    if and wherever such third-party acknowledgments normally appear.
 .
 4. The names "Apache" and "Apache Software Foundation" must
    not be used to endorse or promote products derived from this
    software without prior written permission. For written
    permission, please contact apache@apache.org.
 .
 5. Products derived from this software may not be called "Apache",
    nor may "Apache" appear in their name, without prior written
    permission of the Apache Software Foundation.
 .
 THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESSED 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 APACHE SOFTWARE FOUNDATION OR
 ITS CONTRIBUTORS 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: LGPL-2.1
 On Debian systems the full text of the LGPL-3 can be found in
 /usr/share/common-licenses/LGPL-2.1

License: AML
 IMPORTANT:  This Apple software is supplied to you by Apple Computer,
 Inc. ("Apple") in consideration of your agreement to the following
 terms, and your use, installation, modification or redistribution of
 this Apple software constitutes acceptance of these terms.  If you do
 not agree with these terms, please do not use, install, modify or
 redistribute this Apple software.
 .
 In consideration of your agreement to abide by the following terms, and
 subject to these terms, Apple grants you a personal, non-exclusive
 license, under Apple’s copyrights in this original Apple software (the
 "Apple Software"), to use, reproduce, modify and redistribute the Apple
 Software, with or without modifications, in source and/or binary forms;
 provided that if you redistribute the Apple Software in its entirety
 and without modifications, you must retain this notice and the
 following text and disclaimers in all such redistributions of the Apple
 Software.  Neither the name, trademarks, service marks or logos of
 Apple Computer, Inc. may be used to endorse or promote products derived
 from the Apple Software without specific prior written permission from
 Apple.  Except as expressly stated in this notice, no other rights or
 licenses, express or implied, are granted by Apple herein, including
 but not limited to any patent rights that may be infringed by your
 derivative works or by other works in which the Apple Software may be
 incorporated.
 .
 The Apple Software is provided by Apple on an "AS IS" basis.  APPLE
 MAKES NO WARRANTIES, EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION
 THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY AND FITNESS
 FOR A PARTICULAR PURPOSE, REGARDING THE APPLE SOFTWARE OR ITS USE AND
 OPERATION ALONE OR IN COMBINATION WITH YOUR PRODUCTS.
 .
 IN NO EVENT SHALL APPLE BE LIABLE FOR ANY SPECIAL, INDIRECT, INCIDENTAL
 OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
 BUSINESS INTERRUPTION) ARISING IN ANY WAY OUT OF THE USE, REPRODUCTION,
 MODIFICATION AND/OR DISTRIBUTION OF THE APPLE SOFTWARE, HOWEVER CAUSED
 AND WHETHER UNDER THEORY OF CONTRACT, TORT (INCLUDING NEGLIGENCE),
 STRICT LIABILITY OR OTHERWISE, EVEN IF APPLE HAS BEEN ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE.
