Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: snpEff
Upstream-Contact: Pablo Cingolani <pcingola@users.sourceforge.net>
Source: https://github.com/pcingola/SnpEff/releases
Files-Excluded: */config/OLD
                *.jar
                */papers/*.pdf
                */scripts_build/OLD
                examples
                git
                html/css
                html/js
                html/*.pdf
                html/commonPrint.css
                src/main/java/org/snpeff/fastq/Fastq.java
                src/main/java/org/snpeff/fastq/FastqBuilder.java
                src/main/java/org/snpeff/fastq/FastqVariant.java
Comment: The three last files are provided by biojava4-live. Other files are
 useless or have unclear copyright.

Files: *
Copyright: 2008-2021 Pablo Cingolani <pcingola@users.sourceforge.net>
License: LGPL-3
Comment: The source files are not properly copyrighted but the license is
 clearly stated in html/SnpEff.html as well as on the website, see
 https://pcingola.github.io/SnpEff/download/

Files: src/main/java/net/sf/samtools/tabix/TabixReader.java
Copyright: 2010      Broad Institute
License: Expat

Files: src/main/java/org/broad/*
Copyright: 2007-2011 The Broad Institute of MIT and Harvard
License: LGPL-2.1

Files: src/main/java/org/broad/tribble/*
Copyright: 2007-2009 The Broad Institute, Inc. and the Massachusetts Institute of Technology
License: LGPL-2.1

Files: src/main/java/org/snpeff/collections/ArrayUtil.java
       src/main/java/org/snpeff/collections/BitUtil.java
       src/main/java/org/snpeff/collections/OpenBitSet.java
Copyright: Apache Software Foundation
License: Apache-2.0

Files: debian/*
Copyright: 2012      Andreas Tille <tille@debian.org>
           2020-2021 Pierre Gruet <pgt@debian.org>
License: LGPL-3

License: LGPL-3
 On Debian systems the full text of the LGPL-3 can be found in
 /usr/share/common-licenses/LGPL-3

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-2.1
 On Debian systems the full text of the LGPL-3 can be found in
 /usr/share/common-licenses/LGPL-2.1

License: Apache-2.0
 On Debian systems, the full text of the Apache-2.0 license
 can be found in the file '/usr/share/common-licenses/Apache-2.0'.