This is an automated email from the git hooks/post-receive script. misterc-guest pushed a commit to tag debian/2.3.2.000platform-issues0-8ae7bc0+dfsg1 in repository seqan2.
commit c7ad6053eed63d356b510f13440964931beec788 Merge: 0b62576 f945f14 Author: Michael R. Crusoe <[email protected]> Date: Mon Oct 23 09:35:31 2017 -0700 Updated version 2.3.2.000platform-issues0-8ae7bc0+dfsg1 from 'upstream/2.3.2.000platform-issues0-8ae7bc0+dfsg1' with Debian dir 4715d4eee1613a998c97a4407278a7a4e75e9047 CMakeLists.txt | 5 +- apps/mason2/mason_options.cpp | 38 +- apps/mason2/mason_options.h | 4 + apps/mason2/vcf_materialization.cpp | 7 +- apps/micro_razers/micro_razers.cpp | 1 + apps/seqan_tcoffee/README | 22 +- apps/seqan_tcoffee/seqan_tcoffee.cpp | 37 +- apps/sgip/sgip.cpp | 2 +- apps/splazers/splazers.cpp | 1 + demos/tutorial/a_first_example/final_result.cpp | 22 +- .../a_first_example/final_result.cpp.stdout | 13 +- demos/tutorial/a_first_example/solution_1.cpp | 4 - demos/tutorial/a_first_example/solution_2.cpp | 6 +- .../tutorial/a_first_example/solution_2.cpp.stdout | 2 +- demos/tutorial/a_first_example/solution_3.cpp | 6 +- .../tutorial/a_first_example/solution_3.cpp.stdout | 2 +- demos/tutorial/a_first_example/solution_4.cpp | 4 +- .../tutorial/a_first_example/solution_4.cpp.stdout | 3 +- .../solution_4_templateSubclassing.cpp | 2 - demos/tutorial/a_first_example/solution_5.cpp | 10 +- .../tutorial/a_first_example/solution_5.cpp.stdout | 4 +- demos/tutorial/a_first_example/solution_6.cpp | 20 +- .../tutorial/a_first_example/solution_6.cpp.stdout | 12 +- demos/tutorial/blast_io/write_assignment.cpp | 3 +- demos/tutorial/iterators/assignment_1_solution.cpp | 4 +- demos/tutorial/sequences/base.cpp | 2 +- include/seqan/align.h | 1 + include/seqan/align/dp_algorithm_impl.h | 19 +- include/seqan/align/dp_align_simd_helper.h | 110 +- include/seqan/align/dp_meta_info.h | 2 +- include/seqan/align/dp_profile.h | 12 + include/seqan/align/dp_scout_simd.h | 282 +++- include/seqan/align/dp_traceback_impl.h | 8 +- include/seqan/arg_parse/arg_parse_version_check.h | 16 +- include/seqan/bam_io/bam_alignment_record.h | 49 +- include/seqan/bam_io/bam_index_bai.h | 4 +- include/seqan/bam_io/bam_sam_conversion.h | 2 +- include/seqan/bam_io/read_bam.h | 2 +- include/seqan/basic.h | 3 - include/seqan/basic/alphabet_residue.h | 11 + include/seqan/basic/basic_simd_vector.h | 1671 -------------------- include/seqan/basic/basic_stream.h | 23 +- include/seqan/basic/debug_test_system.h | 8 +- include/seqan/blast/blast_statistics.h | 23 +- .../graph_algorithms/maximum_weighted_matching.h | 246 +++ include/seqan/index/index_bifm_stree.h | 3 + .../seqan/index/index_fm_rank_dictionary_levels.h | 10 - include/seqan/index/index_fm_stree.h | 17 +- include/seqan/index/index_sa_stree.h | 6 +- .../journaled_string_tree_traverser.h | 12 + include/seqan/platform.h | 67 +- include/seqan/reduced_aminoacid.h | 17 +- .../reduced_aminoacid_buchfink11_base.h | 123 ++ .../reduced_aminoacid_buchfink11_tables.h | 155 ++ .../reduced_aminoacid_cannata10_base.h | 120 ++ .../reduced_aminoacid_cannata10_tables.h | 154 ++ .../reduced_aminoacid_li10_base.h | 120 ++ .../reduced_aminoacid_li10_tables.h | 154 ++ .../reduced_aminoacid_murphy5_base.h | 115 ++ .../reduced_aminoacid_murphy5_tables.h | 149 ++ .../reduced_aminoacid_solis10_base.h | 120 ++ .../reduced_aminoacid_solis10_tables.h | 154 ++ include/seqan/score.h | 1 + include/seqan/score/score_simd_wrapper.h | 41 +- include/seqan/simd.h | 124 ++ include/seqan/simd/simd_base.h | 319 ++++ include/seqan/simd/simd_base_seqan_impl.h | 143 ++ include/seqan/simd/simd_base_seqan_impl_avx2.h | 1440 +++++++++++++++++ include/seqan/simd/simd_base_seqan_impl_sse4.2.h | 978 ++++++++++++ include/seqan/simd/simd_base_seqan_interface.h | 389 +++++ include/seqan/simd/simd_base_umesimd_impl.h | 602 +++++++ include/seqan/stream/iostream_bgzf.h | 8 +- include/seqan/stream/tokenization.h | 21 +- include/seqan/version.h | 4 +- .../Infrastructure/Use/CustomBuildSystem.rst | 15 + .../DataStructures/Sequence/StringsAndSegments.rst | 2 +- .../Tutorial/GettingStarted/AFirstExample.rst | 33 +- .../GettingStarted/BackgroundAndMotivation.rst | 2 +- manual/source/seqan.bib | 11 - tests/align/CMakeLists.txt | 3 +- tests/bam_io/test_bam_index.h | 2 + tests/basic/CMakeLists.txt | 7 - tests/basic/test_basic_simd_vector.h | 155 -- tests/blast/test_blast_output.h | 2 +- tests/index/test_index_stree_iterators.cpp | 1 + tests/index/test_stree_iterators.h | 18 + .../test_journaled_string_tree_traverser.cpp | 1 + .../test_journaled_string_tree_traverser.h | 16 + tests/reduced_aminoacid/test_reduced_aminoacid.cpp | 5 + tests/reduced_aminoacid/test_reduced_aminoacid.h | 95 ++ tests/simd/CMakeLists.txt | 48 + .../test_simd_vector.cpp} | 28 +- tests/simd/test_simd_vector.h | 953 +++++++++++ util/cmake/FindSDE.cmake | 81 + util/cmake/FindUmesimd.cmake | 65 + util/cmake/SeqAnBuildSystem.cmake | 52 +- util/cmake/SeqAnContribs.cmake | 2 +- util/cmake/SeqAnSimdUtility.cmake | 611 +++++++ 98 files changed, 8249 insertions(+), 2253 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
