[med-svn] [spades] 01/05: update copyright for new release

Wed Apr 19 13:24:36 UTC 2017

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misterc-guest pushed a commit to branch master
in repository spades.

commit ec8ce0a931bdb6cbbe5562d1ba882063ffae125e
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Wed Apr 19 02:55:13 2017 -0700

    update copyright for new release
---
 debian/copyright | 67 +++++++++++---------------------------------------------
 1 file changed, 13 insertions(+), 54 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 7225ba8..dcf502e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,7 +4,8 @@ Upstream-Contact: spades.support at bioinf.spbau.ru
 Source: http://spades.bioinf.spbau.ru/
 Files-Excluded:
     ext/src/python_libs
-    ext/tools/bwa-*
+    ext/tools/bwa*
+    ext/src/bwa
     ext/include/boost
     ext/include/samtools
     ext/src/samtools/misc/ace2sam
@@ -25,7 +26,7 @@ Files-Excluded:
 
 Files: *
 Copyright: 2011-2014 Saint-Petersburg Academic University
-                2015 Saint Petersburg State University
+           2015-2017 Saint Petersburg State University
 License: GPL-2+
 
 Files: debian/*
@@ -34,7 +35,7 @@ Copyright: 2014-2016 Andreas Tille <tille at debian.org>
                 2016 Sascha Steinbiss <sascha at steinbiss.name>
 License: GPL-2+
 
-Files: src/ionhammer/seqeval/*
+Files: src/projects/ionhammer/seqeval/*
 Copyright: (C) 2012-2013 Ion Torrent Systems, Inc. All Rights Reserved
 License: GPL-2+
 Comment:
@@ -66,7 +67,7 @@ License: GPL-2+
  On Debian systems you can find the full test of the GNU General Public
  License version 2 at /usr/share/common-licenses/GPL-2.
 
-Files: src/hammer/parallel_radix_sort.hpp
+Files: src/projects/hammer/parallel_radix_sort.hpp
 Copyright: (c) 2010 Takuya Akiba
 License: BSD-3-clause-Akiba
  Redistribution and use in source and binary forms, with or without
@@ -97,7 +98,7 @@ License: BSD-3-clause-Akiba
  (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-Files: src/include/xmath.h
+Files: src/common/math/xmath.h
        ext/include/sparsehash/*
 Copyright: (c) 2005 Google Inc.
 License: BSD-3-clause-Google
@@ -219,34 +220,6 @@ License: MIT
 Comment: This file is taken from LLVM's libc++.
  See http://llvm.org/docs/DeveloperPolicy.html#license.
 
-Files: ext/include/nlopt/*
-       ext/src/nlopt/*
-Copyright: (c) 2007-2012 Massachusetts Institute of Technology
-License: MIT
-
-Files: ext/include/nlopt/esch.h
-       ext/src/nlopt/esch/*
-Copyright: (c) 2008-2013 Carlos Henrique da Silva Santos
-License: MIT
-
-Files: ext/include/nlopt/bobyqa.h
-Copyright: (c) 2009 M. J. D. Powell (mjdp at cam.ac.uk)
-           (c) 2010 Massachusetts Institute of Technology
-License: MIT
-
-Files: ext/include/nlopt/cobyla.h
-       ext/src/nlopt/cobyla/*
-Copyright: (c) 1992, Michael J. D. Powell (M.J.D.Powell at damtp.cam.ac.uk)
-           (c) 2004, Jean-Sebastien Roy (js at jeannot.org)
-           (c) 2008, Steven G. Johnson (stevenj at alum.mit.edu)
-License: MIT
-
-Files: ext/src/nlopt/util/mt19937ar.c
-Copyright: (c) 1997-2002 Makoto Matsumoto (m-mat at math.sci.hiroshima-u.ac.jp)
-	   (c) 1997-2002 Takuji Nishimura
-	   (c) 2007,2009 Steven G. Johnson
-License: BSD-3-clause
-
 Files: ext/src/llvm/reg*
 Copyright: (c) 1992, 1993, 1994 Henry Spencer.
            (c) 1992, 1993, 1994 The Regents of the University of California.  All rights reserved.
@@ -285,24 +258,11 @@ Copyright: (c) 2008-2009 Genome Research Ltd.
            (c) 2008 Broad Institute / Massachusetts Institute of Technology
 License: MIT
 
-Files: ext/src/ssw/*
-       ext/include/ssw/*
-Copyright: (c) 2012-1015 Boston College
-License: MIT
-Comment:
- Please find original license attribution for this code at:
- https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
-
 Files: ext/include/city/*
        ext/src/cityhash/*
 Copyright: (c) 2011 Google, Inc.
 License: MIT
 
-Files: ext/include/htrie/*
-       ext/src/htrie/*
-Copyright: (c) 2011 Daniel C. Jones <dcjones at cs.washington.edu>
-License: MIT
-
 Files: ext/include/cxxopts/*
 Copyright: (c) 2014, 2015, 2016 Jarryd Beck
 License: MIT
@@ -334,6 +294,10 @@ Files: ext/include/folly/*
 Copyright: 2014 Facebook, Inc.
 License: Apache-2
 
+Files: ext/include/cuckoo/*
+Copyright: 2013, Carnegie Mellon University and Intel Corporation
+License: Apache-2
+
 License: Apache-2
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
@@ -352,7 +316,7 @@ Files: ext/include/cppformat/*
 Copyright: (c) 2012-2014 Victor Zverovich
 License: BSD-2-clause
 
-Files: src/include/io/mpmc_bounded.hpp
+Files: src/common/io/reads/mpmc_bounded.hpp
 Copyright: (c) 2015 Saint Petersburg State University
            (c) 2011-2014 Saint Petersburg Academic University
            (c) 2011 Dmitry Vyukov. All rights reserved.
@@ -380,6 +344,7 @@ License: BSD-2-clause
  SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 Files: ext/include/getopt_pp/*
+       ext/src/getopt_pp/*
 Copyright: (C) 2007, 2008  Daniel Gutson, FuDePAN
 License: GPL-3+
 
@@ -424,7 +389,7 @@ License: Boost-1
  ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  DEALINGS IN THE SOFTWARE.
 
-Files: src/hammer/quake_correct/gzstream.*
+Files: src/projects/hammer/quake_correct/gzstream.*
 Copyright: (C) 2001 Deepak Bandyopadhyay
            (C) 2001 Lutz Kettner
 License: LGPL-2.1+
@@ -476,9 +441,3 @@ License: BSDlike-libbzip2
  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.
-
-Files: ext/src/htrie/murmurhash*
-Copyright: Austin Appleby
-License: public-domain
- The original C++ code was placed in the public domain by its author,
- Austin Appleby.

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