[med-svn] [seqan2] 01/02: Updated version 2.3.2.000platform-issues0-8ae7bc0+dfsg1 from 'upstream/2.3.2.000platform-issues0-8ae7bc0+dfsg1'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Oct 24 07:15:17 UTC 2017
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 <michael.crusoe at gmail.com>
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
More information about the debian-med-commit
mailing list