[med-svn] [seqan2] branch upstream-experimental updated (9f5dc02 -> 817a28f)

[Michael Crusoe]

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

      from  9f5dc02   New upstream version 2.3.2.000platform-issues8-6f85721+dfsg
       new  817a28f   New upstream version 2.3.2.000platform-issues9-028fd79+dfsg

The 1 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 +-
 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 +-
 63 files changed, 578 insertions(+), 257 deletions(-)

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