[med-svn] [seqan2] 01/02: Update upstream source from tag 'upstream/2.3.2.001platform-issues10-6f85721+dfsg'

[Michael Crusoe]

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misterc-guest pushed a commit to tag debian/2.3.2.001platform-issues10-6f85721+dfsg-1
in repository seqan2.

commit 9b11d0813b84789193ecbef3f30dfb6250e3f195
Merge: b19650a 4955144
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Wed Jan 3 09:13:44 2018 -0800

    Update upstream source from tag 'upstream/2.3.2.001platform-issues10-6f85721+dfsg'
    
    Update to upstream version '2.3.2.001platform-issues10-6f85721+dfsg'
    with Debian dir 44be9185e1cf97bc5cc6e5e69231ab333c79c707

 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, 257 insertions(+), 578 deletions(-)

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