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commit 8e1ffee0ea94714ad2225baf4443bd75229ec7e0 Merge: 04b9d2f 817a28f Author: Michael R. Crusoe <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqan2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
