[med-svn] [seqan2] 01/02: Updated version 2.3.2+dfsg from 'upstream/2.3.2+dfsg'

[Michael Crusoe]

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misterc-guest pushed a commit to tag debian/2.3.2+dfsg-1
in repository seqan2.

commit 5db3cf7350548224d73eef5b31e4083c5f76c6e9
Merge: c369494 b70ac79
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Thu Sep 28 07:46:18 2017 -0700

    Updated version 2.3.2+dfsg from 'upstream/2.3.2+dfsg'
    
    with Debian dir 0811ffed9627e5c0994a1eff090e137026ff636c

 CHANGELOG.rst                                      |  16 ++
 README.rst                                         |   4 +-
 apps/alf/CMakeLists.txt                            |   2 +-
 apps/bs_tools/CMakeLists.txt                       |   7 +-
 apps/dfi/CMakeLists.txt                            |   2 +-
 apps/fiona/CMakeLists.txt                          |   2 +-
 apps/fiona/fiona.cpp                               |  30 ++-
 apps/fx_tools/CMakeLists.txt                       |   2 +-
 apps/gustaf/CMakeLists.txt                         |   2 +-
 apps/insegt/CMakeLists.txt                         |   2 +-
 apps/mason2/CMakeLists.txt                         |   2 +-
 apps/micro_razers/CMakeLists.txt                   |   2 +-
 apps/ngs_roi/CMakeLists.txt                        |   2 +-
 apps/pair_align/CMakeLists.txt                     |   2 +-
 apps/param_chooser/CMakeLists.txt                  |   2 +-
 apps/rabema/CMakeLists.txt                         |   2 +-
 apps/razers/CMakeLists.txt                         |   2 +-
 apps/razers3/CMakeLists.txt                        |   2 +-
 apps/rep_sep/CMakeLists.txt                        |   2 +-
 apps/sak/CMakeLists.txt                            |   2 +-
 apps/sam2matrix/CMakeLists.txt                     |   2 +-
 apps/samcat/CMakeLists.txt                         |   2 +-
 apps/searchjoin/CMakeLists.txt                     |   2 +-
 apps/searchjoin/db.h                               |  16 +-
 apps/searchjoin/join.cpp                           |  17 +-
 apps/searchjoin/search.cpp                         |  16 +-
 apps/seqan_tcoffee/CMakeLists.txt                  |   2 +-
 apps/seqcons2/CMakeLists.txt                       |   2 +-
 apps/sgip/CMakeLists.txt                           |   2 +-
 apps/snp_store/CMakeLists.txt                      |   2 +-
 apps/splazers/CMakeLists.txt                       |   2 +-
 apps/stellar/CMakeLists.txt                        |   2 +-
 apps/tree_recon/CMakeLists.txt                     |   2 +-
 apps/yara/CMakeLists.txt                           |   2 +-
 .../parsing_command_line_arguments/base.cpp        |  97 ++++++++++
 .../parsing_command_line_arguments/base.cpp.stdout |   0
 dox/CMakeLists.txt                                 |   4 +-
 dox/{dox_only.sh => dox_only.sh.in}                |   0
 dox/{run.sh => run.sh.in}                          |   0
 include/seqan/align/dp_scout_simd.h                |   4 +-
 include/seqan/arg_parse/arg_parse_argument.h       |  64 +++---
 include/seqan/arg_parse/arg_parse_ctd_support.h    |  56 +++++-
 include/seqan/arg_parse/arg_parse_version_check.h  |  24 ++-
 include/seqan/index/index_bidirectional_stree.h    |   8 +-
 include/seqan/index/index_bifm_stree.h             |  28 +--
 .../journaled_string_tree_impl.h                   |   1 +
 include/seqan/seq_io/sequence_file.h               |  12 +-
 include/seqan/version.h                            |   2 +-
 .../Infrastructure/Use/CustomBuildSystem.rst       |   4 +-
 .../source/Infrastructure/Use/FindSeqAnCMake.rst   |  44 ++++-
 manual/source/Tutorial/Applications/Lambda.rst.bak |  10 -
 manual/source/Tutorial/Applications/Yara.rst.bak   |  10 -
 manual/source/Tutorial/Applications/index.rst.bak  |  13 --
 .../GettingStarted/ParsingCommandLineArguments.rst | 215 ++++++++++++---------
 tests/arg_parse/test_app.ctd                       |  18 +-
 tests/arg_parse/test_arg_parse_ctd_support.h       |   1 +
 tests/arg_parse/test_arg_parse_version_check.h     |   2 +-
 tests/index/test_index_bifm.cpp                    |  14 +-
 .../platform/test_platform_range_based_for_loops.h |   2 -
 tests/seq_io/test_tag_select_intersect.h           |  21 +-
 util/cmake/FindSeqAn.cmake                         |   1 +
 util/cmake/SeqAnConsistentFPFlags.cmake            |  59 ++++++
 util/pkgconfig/seqan.pc.in                         |   2 +-
 util/travis/linux-cibuild.sh                       |   3 +
 64 files changed, 560 insertions(+), 319 deletions(-)

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