Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://picard.svn.sourceforge.net/viewvc/picard/tags/1.110/
Comment: Some source files are removed, see debian/rules.

Files: *
Copyright: © 2009–2014 The Broad Institute
License: MIT
 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.

Files: src/java/net/sf/samtools/util/DateParser.java
Copyright: 2000 MIT, INRIA and Keio
License: W3C-Software
 W3C IPR SOFTWARE NOTICE
 .
 Copyright 1995-1998 World Wide Web Consortium, (Massachusetts Institute of
 Technology, Institut National de Recherche en Informatique et en
 Automatique, Keio University). All Rights Reserved.
 http://www.w3.org/Consortium/Legal/
 .
 This W3C work (including software, documents, or other related items) is
 being provided by the copyright holders under the following license. By
 obtaining, using and/or copying this work, you (the licensee) agree that you
 have read, understood, and will comply with the following terms and
 conditions:
 .
 Permission to use, copy, and modify this software and its documentation,
 with or without modification, for any purpose and without fee or royalty is
 hereby granted, provided that you include the following on ALL copies of the
 software and documentation or portions thereof, including modifications,
 that you make:
 .
   1. The full text of this NOTICE in a location viewable to users of the
      redistributed or derivative work.
   2. Any pre-existing intellectual property disclaimers, notices, or terms
      and conditions. If none exist, a short notice of the following form
      (hypertext is preferred, text is permitted) should be used within the
      body of any redistributed or derivative code: "Copyright World Wide
      Web Consortium, (Massachusetts Institute of Technology, Institut
      National de Recherche en Informatique et en Automatique, Keio
      University). All Rights Reserved. http://www.w3.org/Consortium/Legal/"
   3. Notice of any changes or modifications to the W3C files, including the
      date changes were made. (We recommend you provide URIs to the location
      from which the code is derived).
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 In addition, creators of derivitive works must include the full text of this
 NOTICE in a location viewable to users of the derivitive work.
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 THIS SOFTWARE AND DOCUMENTATION IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS
 MAKE NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT
 LIMITED TO, WARRANTIES OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR
 PURPOSE OR THAT THE USE OF THE SOFTWARE OR DOCUMENTATION WILL NOT INFRINGE
 ANY THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS.
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 COPYRIGHT HOLDERS WILL NOT BE LIABLE FOR ANY DIRECT, INDIRECT, SPECIAL OR
 CONSEQUENTIAL DAMAGES ARISING OUT OF ANY USE OF THE SOFTWARE OR
 DOCUMENTATION.
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 The name and trademarks of copyright holders may NOT be used in advertising
 or publicity pertaining to the software without specific, written prior
 permission. Title to copyright in this software and any associated
 documentation will at all times remain with copyright holders.

Files: etc/test/junit-noframes.xsl
Copyright: 2001-2004 The Apache Software Foundation
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’.

Files: src/c/inteldeflater/IntelDeflater.c
 src/java/net/sf/samtools/util/zip/IntelDeflater.java
 src/java/net/sf/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
 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’.

Files: src/java/net/sf/samtools/seekablestream/SeekableFTPStream.java
 src/java/net/sf/samtools/seekablestream/SeekableFTPStreamHelper.java
 src/java/net/sf/samtools/seekablestream/SeekableFileStream.java
 src/java/net/sf/samtools/util/ftp/FTPClient.java
 src/java/net/sf/samtools/util/ftp/FTPReply.java
 src/java/net/sf/samtools/util/ftp/FTPStream.java
 src/java/net/sf/samtools/util/ftp/FTPUtils.java
 src/java/org/broad/tribble/AbstractFeatureReader.java
 src/java/org/broad/tribble/AsciiFeatureCodec.java
 src/java/org/broad/tribble/CloseableTribbleIterator.java
 src/java/org/broad/tribble/FeatureCodec.java
 src/java/org/broad/tribble/FeatureReader.java
 src/java/org/broad/tribble/index/AbstractIndex.java
 src/java/org/broad/tribble/index/interval/Interval.java
 src/java/org/broad/tribble/index/interval/IntervalIndexCreator.java
 src/java/org/broad/tribble/index/interval/IntervalTree.java
 src/java/org/broad/tribble/index/interval/IntervalTreeIndex.java
 src/java/org/broad/tribble/index/linear/LinearIndex.java
 src/java/org/broad/tribble/readers/AsciiLineReader.java
 src/java/org/broad/tribble/readers/PositionalBufferedStream.java
 src/java/org/broad/tribble/util/HTTPHelper.java
 src/java/org/broad/tribble/util/URLHelper.java
 src/tests/java/org/broad/tribble/index/interval/IntervalTreeTest.java
 src/tests/java/org/broad/tribble/index/linear/LinearIndexTest.java
Comment: git grep 'lgpl-2.1' | cut -f 1 -d ':'
 git grep 'lgpl-2.1' | cut -f 1 -d ':' | xargs grep -h Copyright
Copyright: * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2009 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2009-2010 by The Broad Institute, Inc.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2009-2010 by The Broad Institute, Inc.
 * Copyright (c) 2007-2009 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2009 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * Copyright (c) 2009-2010 by The Broad Institute, Inc.
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

Files: debian/*
Copyright: 2010 Shaun Jackman <sjackman@debian.org>
           2013 Olivier Sallou <osallou@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.
