[med-svn] [seqan2] 04/07: Update upstream source from tag 'upstream/2.3.2.000platform-issues9-028fd79+dfsg'

[Michael Crusoe]

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

commit 8e1ffee0ea94714ad2225baf4443bd75229ec7e0
Merge: 04b9d2f 817a28f
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Wed Dec 20 07:28:11 2017 -0800

    Update upstream source from tag 'upstream/2.3.2.000platform-issues9-028fd79+dfsg'
    
    Update to upstream version '2.3.2.000platform-issues9-028fd79+dfsg'
    with Debian dir c25558f6b078c9a290a77ec92bb85bbb8df1f95b

 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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