[med-svn] [lambda-align] 11/15: Merge tag 'upstream/1.9.0'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository lambda-align.

commit a7b0479039c40debc48fed0fc0eb2efe731f53eb
Merge: a1d1169 f5ebbcd
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Aug 18 21:28:15 2016 +0000

    Merge tag 'upstream/1.9.0'
    
    Upstream version 1.9.0

 .gitmodules                                        |    3 +
 .travis.yml                                        |   88 +-
 CMakeLists.txt                                     |   50 +-
 COPYING.rst                                        |   27 -
 LICENSE-AGPL3.rst                                  |  671 ++++++++++
 include/seqan/LICENSE => LICENSE-BSD.rst           |   26 +-
 LICENSE-GPL3.rst                                   |  704 ----------
 LICENSE.rst                                        |   45 +
 README.rst                                         |  143 +-
 include/seqan/.travis.yml                          |   30 -
 include/seqan/util/cmake/CMakeFindJavaCommon.cmake |   40 -
 .../util/cmake/CMakeMacroParseArguments.cmake      |  138 --
 include/seqan/util/cmake/CTestConfig.cmake         |   13 -
 include/seqan/util/cmake/FeatureSummary.cmake      |  117 --
 include/seqan/util/cmake/FindBZip2.cmake           |   61 -
 include/seqan/util/cmake/FindCXX11.cmake           |   39 -
 include/seqan/util/cmake/FindCXX14.cmake           |   29 -
 include/seqan/util/cmake/FindGitInfo.cmake         |   64 -
 include/seqan/util/cmake/FindJava.cmake            |  228 ----
 include/seqan/util/cmake/FindOpenCL.cmake          |   79 --
 include/seqan/util/cmake/FindOpenMP.cmake          |  137 --
 .../util/cmake/FindPackageHandleStandardArgs.cmake |  261 ----
 include/seqan/util/cmake/FindSeqAn.cmake           |  480 -------
 include/seqan/util/cmake/FindSphinx.cmake          |  145 ---
 include/seqan/util/cmake/FindTBB/FindTBB.cmake     |  208 ---
 include/seqan/util/cmake/FindTBB/README            |    6 -
 include/seqan/util/cmake/FindZLIB.cmake            |  107 --
 include/seqan/util/cmake/GetCurrentDate.cmake      |   57 -
 include/seqan/util/cmake/GetCurrentDate.cpp        |   52 -
 include/seqan/util/cmake/LibFindMacros.cmake       |   99 --
 include/seqan/util/cmake/README                    |   84 --
 include/seqan/util/cmake/SeqAnBuildSystem.cmake    |  731 -----------
 include/seqan/util/cmake/SeqAnContribs.cmake       |  117 --
 include/seqan/util/cmake/SeqAnCtdSetup.cmake       |  242 ----
 .../seqan/util/cmake/SeqAnUsabilityAnalyzer.cmake  |   98 --
 include/seqan/util/cmake/SeqAnVersion.cpp          |   48 -
 include/seqan/util/cmake/SetCPackSystemName.cmake  |   51 -
 include/seqan/util/cmake/ctd/COPYRIGHT             |    2 -
 include/seqan/util/cmake/ctd/DESCRIPTION           |    7 -
 include/seqan/util/cmake/ctd/LICENSE               |   31 -
 .../cmake/ctd/configure_profile_properties.cmake   |   13 -
 include/seqan/util/cmake/ctd/icons/app.png         |  Bin 3931 -> 0 bytes
 include/seqan/util/cmake/ctd/icons/category.png    |  Bin 2978 -> 0 bytes
 include/seqan/util/cmake/ctd/icons/splash.png      |  Bin 9838 -> 0 bytes
 include/seqan/util/cmake/ctd/mime.types            |   37 -
 include/seqan/util/cmake/ctd/mimetypes.xml         |   23 -
 include/seqan/util/cmake/ctd/plugin.properties.in  |   15 -
 include/seqan/util/cmake/package.cmake             |   96 --
 include/seqan/util/colornvcc                       |  259 ----
 include/seqan/util/ctd2galaxy.py                   |  192 ---
 include/seqan/util/linux_binary_tests.sh           |  171 ---
 include/seqan/util/makefile_project/Makefile       |   15 -
 include/seqan/util/makefile_project/Makefile.rules |   17 -
 include/seqan/util/makefile_project/README         |    1 -
 include/seqan/util/makefile_project/debug/Makefile |    3 -
 .../seqan/util/makefile_project/release/Makefile   |    3 -
 include/seqan/util/makefile_project/src/main.cpp   |   11 -
 .../seqan/util/raw_cmake_project/CMakeLists.txt    |   11 -
 include/seqan/util/raw_cmake_project/README        |    2 -
 .../util/raw_cmake_project/src/CMakeLists.txt      |   12 -
 include/seqan/util/raw_cmake_project/src/main.cpp  |   12 -
 src/CMakeLists.txt                                 |  240 ++--
 src/alph.hpp                                       |  237 ----
 src/holders.hpp                                    |  316 ++---
 src/lambda.cpp                                     |  236 ++--
 src/lambda.hpp                                     | 1369 +++++++++++++++-----
 src/lambda_indexer.cpp                             |   47 +-
 src/lambda_indexer.hpp                             |  314 ++---
 src/lambda_indexer_misc.hpp                        |   19 +-
 src/match.hpp                                      |   87 +-
 src/misc.hpp                                       |   57 +-
 src/options.hpp                                    |  411 ++++--
 src/output.hpp                                     |  213 ++-
 src/radix_inplace.h                                |    2 +-
 tests/CMakeLists.txt                               |   21 +-
 tests/search_test_outfile.md5sums.gz               |  Bin 1082 -> 1082 bytes
 76 files changed, 3112 insertions(+), 6908 deletions(-)

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