[med-svn] [seqan2] branch experimental updated (cbb003f -> b19650a)

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

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

      from  cbb003f   Another update from upstream
       new  864446e   force rebuild
       new  04b9d2f   keep async, try a regular release
       new  817a28f   New upstream version 2.3.2.000platform-issues9-028fd79+dfsg
       new  8e1ffee   Update upstream source from tag 'upstream/2.3.2.000platform-issues9-028fd79+dfsg'
       new  efe35a2   another update from upstream
       new  30d3c43   switch to -DCMAKE_BUILD_TYPE=Release as per upstream
       new  b19650a   cleanup build flags

The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 apps/alf/CMakeLists.txt                            |   2 +-
 apps/alf/alf.cpp                                   |   2 +-
 apps/bs_tools/CMakeLists.txt                       |   2 +-
 apps/dfi/CMakeLists.txt                            |   2 +-
 apps/fiona/CMakeLists.txt                          |   2 +-
 apps/fiona/compute_gain.cpp                        |   6 +-
 apps/fx_tools/CMakeLists.txt                       |   2 +-
 apps/gustaf/CMakeLists.txt                         |   2 +-
 apps/insegt/CMakeLists.txt                         |   2 +-
 apps/mason2/CMakeLists.txt                         |   2 +-
 apps/mason2/mason_genome.cpp                       |   2 +-
 apps/mason2/mason_variator.cpp                     |  10 +-
 apps/micro_razers/CMakeLists.txt                   |   2 +-
 apps/ngs_roi/CMakeLists.txt                        |   4 +-
 apps/pair_align/CMakeLists.txt                     |   2 +-
 apps/param_chooser/CMakeLists.txt                  |   2 +-
 apps/rabema/CMakeLists.txt                         |   4 +-
 apps/rabema/rabema_build_gold_standard.cpp         |   2 +-
 apps/rabema/rabema_evaluate.cpp                    |   4 +-
 apps/razers/CMakeLists.txt                         |   2 +-
 apps/razers3/CMakeLists.txt                        |   2 +-
 apps/rep_sep/CMakeLists.txt                        |   2 +-
 apps/sak/CMakeLists.txt                            |   4 +-
 apps/sam2matrix/CMakeLists.txt                     |   2 +-
 apps/samcat/CMakeLists.txt                         |   2 +-
 apps/searchjoin/CMakeLists.txt                     |   2 +-
 apps/searchjoin/db.h                               |   8 +-
 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/stellar/stellar.cpp                           |   2 +-
 apps/tree_recon/CMakeLists.txt                     |   2 +-
 apps/yara/CMakeLists.txt                           |   2 +-
 debian/changelog                                   |  16 ++
 debian/control                                     |   2 +-
 debian/rules                                       |  31 ++--
 debian/source/lintian-overrides                    |   2 +-
 dox/CMakeLists.txt                                 |   2 +-
 .../align/local_alignment_waterman_eggert_impl.h   |  39 +++--
 include/seqan/arg_parse/arg_parse_argument.h       |  36 ++++-
 include/seqan/arg_parse/tool_doc.h                 |   7 +
 include/seqan/bam_io/bam_alignment_record_util.h   |   2 +-
 include/seqan/index/index_base.h                   |   2 +-
 include/seqan/index/index_fm_compressed_sa.h       |   6 +-
 include/seqan/index/index_fm_lf_table.h            |   2 +-
 .../seqan/index/index_fm_rank_dictionary_base.h    |   2 +-
 .../seqan/index/index_fm_rank_dictionary_levels.h  |   6 +-
 .../seqan/index/index_fm_rank_dictionary_naive.h   |   2 +-
 include/seqan/index/index_qgram.h                  |   2 +-
 include/seqan/modifier/modifier_padding.h          |  51 +++++-
 include/seqan/platform.h                           |   4 +-
 include/seqan/seeds/seeds_global_chaining.h        | 162 +++++++++++--------
 include/seqan/stream/iter_stream.h                 | 178 ++++++++++++---------
 manual/source/Infrastructure/Use/Install.rst       |  42 ++---
 tests/align/test_alignment_algorithms_local.h      |  47 ++++++
 .../align/test_alignment_algorithms_local_banded.h |  32 ++++
 tests/arg_parse/test_arg_parse.cpp                 |   1 +
 tests/arg_parse/test_arg_parse_argument.h          |  28 ++++
 tests/modifier/test_modifier.cpp                   |   3 +-
 tests/modifier/test_modifier_string_padding.h      |  24 +++
 tests/seeds/test_seeds_global_chaining.cpp         |  26 +++
 util/cmake/SeqAnBuildSystem.cmake                  |  25 ++-
 util/pkgconfig/seqan.pc.in                         |   4 +-
 util/skel/app_template/CMakeLists.txt              |   2 +-
 67 files changed, 605 insertions(+), 281 deletions(-)

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