[med-svn] [seqan2] branch master updated (c369494 -> 6d28a62)

[Michael Crusoe]

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misterc-guest pushed a change to branch master
in repository seqan2.

      from  c369494   make build reproducible
      adds  9a4a748   New upstream version 2.2.0+dfsg
      adds  c804db8   New upstream version 2.3.0~0.20161011~73a5aaf+dfsg
      adds  1d7cc22   New upstream version 2.3.0~0.20161019~af07bc1+dfsg
      adds  d315ded   New upstream version 2.3.1+dfsg
      adds  b70ac79   New upstream version 2.3.2+dfsg
      adds  5db3cf7   Updated version 2.3.2+dfsg from 'upstream/2.3.2+dfsg'
      adds  6d28a62   re-enable armel

No new revisions were added by this update.

Summary of changes:
 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 +-
 debian/changelog                                   |   9 +
 debian/control                                     |   6 +-
 debian/copyright                                   |   1 -
 debian/patches/series                              |   1 -
 debian/patches/skip-SEQAN_PKGCFG_CFLAGS            |  12 --
 debian/rules                                       |   6 +-
 debian/source.lintian-overrides                    |   1 +
 .../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 +
 ...stemName.cmake => SeqAnConsistentFPFlags.cmake} |  57 +++---
 util/pkgconfig/seqan.pc.in                         |   2 +-
 util/travis/linux-cibuild.sh                       |   3 +
 71 files changed, 542 insertions(+), 371 deletions(-)
 delete mode 100644 debian/patches/skip-SEQAN_PKGCFG_CFLAGS
 create mode 100644 debian/source.lintian-overrides
 create mode 100644 demos/tutorial/parsing_command_line_arguments/base.cpp
 copy apps/bs_tools/tests/bisar_out_pe_0.txt => demos/tutorial/parsing_command_line_arguments/base.cpp.stdout (100%)
 rename dox/{dox_only.sh => dox_only.sh.in} (100%)
 mode change 100755 => 100644
 rename dox/{run.sh => run.sh.in} (100%)
 mode change 100755 => 100644
 delete mode 100644 manual/source/Tutorial/Applications/Lambda.rst.bak
 delete mode 100644 manual/source/Tutorial/Applications/Yara.rst.bak
 delete mode 100644 manual/source/Tutorial/Applications/index.rst.bak
 create mode 100644 util/cmake/FindSeqAn.cmake
 copy util/cmake/{SetCPackSystemName.cmake => SeqAnConsistentFPFlags.cmake} (59%)

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