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commit 26d12351c8b86df7153119dc0fb9b24ba986631c Merge: 5f32821 7e3cc84 Author: Michael R. Crusoe <[email protected]> Date: Mon Feb 5 06:53:27 2018 -0800 Merge branch 'experimental' CHANGELOG.rst | 57 +- CMakeLists.txt | 11 +- README.rst | 15 +- apps/alf/CMakeLists.txt | 2 +- apps/alf/README | 8 +- apps/alf/alf.cpp | 2 +- apps/bs_tools/CMakeLists.txt | 2 +- apps/bs_tools/bisar.h | 2 +- apps/bs_tools/casbar.cpp | 10 +- apps/bs_tools/casbar.h | 4 +- apps/bs_tools/casbar_consensus_realign.h | 2 +- apps/bs_tools/casbar_score.h | 42 +- apps/dfi/CMakeLists.txt | 2 +- apps/dfi/README | 14 +- apps/fiona/CMakeLists.txt | 2 +- apps/fiona/compute_gain.cpp | 11 +- apps/fiona/fiona.cpp | 36 +- apps/fx_tools/CMakeLists.txt | 2 +- apps/gustaf/CMakeLists.txt | 2 +- apps/gustaf/README | 6 +- apps/gustaf/create_stellarmatches_from_file.h | 6 +- apps/gustaf/msplazer.h | 42 +- apps/gustaf/msplazer_algorithms.h | 10 +- apps/gustaf/msplazer_out.h | 39 +- apps/insegt/CMakeLists.txt | 2 +- apps/insegt/README | 14 +- apps/insegt/base.h | 6 +- apps/insegt/create_gff.h | 4 +- apps/insegt/fusion.h | 46 +- apps/insegt/overlap_module.h | 32 +- apps/mason2/CMakeLists.txt | 2 +- apps/mason2/external_split_merge.cpp | 6 +- apps/mason2/external_split_merge.h | 6 +- apps/mason2/fragment_generation.h | 2 + apps/mason2/genomic_variants.cpp | 18 +- apps/mason2/mason_genome.cpp | 2 +- apps/mason2/mason_materializer.cpp | 2 +- apps/mason2/mason_options.cpp | 38 +- apps/mason2/mason_options.h | 4 + apps/mason2/mason_simulator.cpp | 4 +- apps/mason2/mason_splicing.cpp | 18 +- apps/mason2/mason_variator.cpp | 38 +- apps/mason2/vcf_materialization.cpp | 7 +- apps/micro_razers/CMakeLists.txt | 2 +- apps/micro_razers/README | 14 +- apps/micro_razers/micro_razers.cpp | 1 + apps/ngs_roi/CMakeLists.txt | 9 +- apps/ngs_roi/project_spliced.cpp | 6 +- apps/ngs_roi/roi_feature_projection.cpp | 2 +- apps/pair_align/CMakeLists.txt | 7 +- apps/pair_align/lib/pair_align_lib.cpp | 2 +- apps/param_chooser/CMakeLists.txt | 2 +- apps/rabema/CMakeLists.txt | 4 +- apps/rabema/rabema_build_gold_standard.cpp | 14 +- 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test_align_simd_global_equal_length.cpp} | 26 +- ... => test_align_simd_global_variable_length.cpp} | 21 +- tests/align/test_align_simd_local.h | 122 ++ ....cpp => test_align_simd_local_equal_length.cpp} | 19 +- ...p => test_align_simd_local_variable_length.cpp} | 18 +- .../test_alignment_algorithms_band_position.h | 96 +- tests/align/test_alignment_algorithms_local.h | 47 + .../align/test_alignment_algorithms_local_banded.h | 32 + .../align/test_alignment_dp_adapt_tracesegments.h | 80 +- tests/align/test_alignment_dp_cell.h | 2 +- tests/align/test_alignment_dp_formula.h | 1326 +++++++++------ tests/align/test_alignment_dp_matrix.h | 2 +- tests/align/test_alignment_dp_matrix_navigator.h | 1704 ++++---------------- tests/align/test_alignment_dp_trace_segment.h | 52 +- tests/align/test_alignment_dp_traceback.h | 395 +++-- tests/align/test_mock.h | 240 +++ tests/align_parallel/CMakeLists.txt | 78 + .../test_align_parallel_algorithm.cpp} | 26 +- .../test_align_parallel_data_structures.cpp} | 45 +- .../test_align_parallel_interface.cpp} | 2 +- .../align_parallel/test_align_parallel_interface.h | 168 ++ .../test_align_parallel_wavefront_alignment.h | 183 +++ .../test_align_wavefront_alignment_scheduler.h | 266 +++ .../test_align_wavefront_alignment_thread_local.h} | 85 +- .../test_align_wavefront_intermediate_dp_result.h | 121 ++ .../test_align_wavefront_task_scheduler.h} | 99 +- tests/arg_parse/test_arg_parse.cpp | 1 + tests/arg_parse/test_arg_parse_argument.h | 28 + tests/arg_parse/test_arg_parse_ctd_support.h | 3 +- tests/bam_io/test_bam_file.h | 26 +- tests/bam_io/test_bam_index.h | 17 +- tests/bam_io/test_bam_io.cpp | 2 +- tests/bam_io/test_bam_sam_conversion.h | 11 + tests/bam_io/test_read_bam.h | 10 +- tests/bam_io/test_write_bam.h | 6 +- tests/basic/CMakeLists.txt | 7 - tests/basic/test_basic.cpp | 1 - tests/basic/test_basic_aggregate.h | 5 +- tests/basic/test_basic_alphabet.cpp | 6 +- tests/basic/test_basic_alphabet.h | 50 +- tests/basic/test_basic_alphabet_adapt_builtins.h | 199 --- tests/basic/test_basic_alphabet_math.h | 29 +- tests/basic/test_basic_alphabet_residue.h | 74 +- tests/basic/test_basic_concept.cpp | 4 +- tests/basic/test_basic_concepts.h | 39 + tests/basic/test_basic_exception.h | 6 +- tests/basic/test_basic_iterator.h | 2 +- tests/basic/test_basic_simd_vector.h | 155 -- tests/bed_io/test_bed_io.cpp | 8 +- tests/blast/test_blast_input.h | 8 +- tests/blast/test_blast_output.h | 2 +- tests/consensus/test_consensus.h | 27 +- tests/consensus/test_consensus_realign.h | 5 +- tests/gff_io/test_gff_io.h | 37 +- tests/index/CMakeLists.txt | 6 +- .../test_find2_index_approx.cpp} | 21 +- tests/index/test_find2_index_approx.h | 489 ++++++ tests/index/test_index_bifm.cpp | 16 +- tests/index/test_index_creation.h | 6 +- tests/index/test_index_fm_rank_dictionary.cpp | 7 +- tests/index/test_index_helpers.h | 8 +- tests/index/test_index_stree_iterators.cpp | 1 + tests/index/test_qgram_index.h | 23 +- tests/index/test_sa_bwtwalk.h | 2 +- tests/index/test_stree_iterators.h | 18 + tests/journaled_string_tree/test_delta_map.h | 14 +- .../test_journaled_string_tree.h | 2 +- .../test_journaled_string_tree_traverser.cpp | 1 + .../test_journaled_string_tree_traverser.h | 16 + tests/misc/test_misc.cpp | 6 +- tests/modifier/test_modifier.cpp | 3 +- tests/modifier/test_modifier_string_padding.h | 24 + .../test_multiple_translation_units.cpp | 1 + .../test_multiple_translation_units_2.cpp | 1 + tests/parallel/CMakeLists.txt | 4 +- tests/parallel/test_parallel.cpp | 21 + .../test_parallel_enumerable_thread_local.h | 217 +++ tests/parallel/test_parallel_thread_pool.h | 151 ++ tests/parse_lm/test_parse_lm.h | 2 +- tests/reduced_aminoacid/test_reduced_aminoacid.cpp | 5 + tests/reduced_aminoacid/test_reduced_aminoacid.h | 95 ++ tests/rna_io/CMakeLists.txt | 4 +- tests/roi_io/test_roi_io.cpp | 8 +- tests/score/test_score.cpp | 9 +- tests/seeds/test_align_banded_chain_impl.cpp | 2 +- tests/seeds/test_seeds_global_chaining.cpp | 26 + tests/seq_io/test_fai_index.h | 24 +- tests/seq_io/test_sequence_file.h | 36 +- tests/sequence/test_sequence.h | 53 +- tests/sequence/test_string_packed_extension.h | 4 +- tests/sequence/test_string_set.h | 67 +- tests/{rna_io => simd}/CMakeLists.txt | 30 +- .../test_simd_vector.cpp} | 28 +- tests/simd/test_simd_vector.h | 979 +++++++++++ tests/statistics/test_statistics_base.h | 3 +- tests/store/test_store_io.h | 92 +- tests/store/test_store_io_bam.h | 10 +- tests/stream/test_stream_lexical_cast.h | 4 +- tests/stream/test_stream_tokenization.h | 60 +- tests/stream/test_stream_virtual_stream.h | 15 +- tests/tabix_io/test_tabix_io.h | 11 +- tests/translation/test_translation.h | 41 +- tests/ucsc_io/test_ucsc_io.cpp | 24 +- tests/vcf_io/example_records_with_errors.vcf | 5 +- tests/vcf_io/test_vcf_io.h | 46 +- util/cmake/FindSDE.cmake | 81 + util/cmake/FindUmesimd.cmake | 65 + util/cmake/SeqAnBuildSystem.cmake | 101 +- util/cmake/SeqAnContribs.cmake | 113 +- util/cmake/SeqAnSimdUtility.cmake | 647 ++++++++ util/cmake/seqan-config.cmake | 31 +- util/pkgconfig/seqan.pc.in | 4 +- util/py_lib/CMakeLists.txt | 5 + util/skel/app_template/CMakeLists.txt | 2 +- util/travis/linux-cibuild.cmake | 1 - util/travis/linux-cibuild.sh | 5 + 539 files changed, 25905 insertions(+), 11231 deletions(-) diff --cc debian/changelog index a0976d7,e539765..e646631 --- a/debian/changelog +++ b/debian/changelog @@@ -1,21 -1,158 +1,176 @@@ + seqan2 (2.4.0~rc2+dfsg-1) experimental; urgency=medium + + * Testing upstream's 3rd formal release candidate for 2.4.0 + * debian/rules: use --max-parallel to more cleanly limit parallel building + + -- Michael R. Crusoe <[email protected]> Wed, 31 Jan 2018 22:23:03 -0800 + + seqan2 (2.4.0~rc1+dfsg-2) experimental; urgency=medium + + * debian/rules: Drop amd64, mips, mipsel to -j3 to save memory + + -- Michael R. Crusoe <[email protected]> Wed, 31 Jan 2018 04:16:59 -0800 + + seqan2 (2.4.0~rc1+dfsg-1) experimental; urgency=medium + + * Testing upstream's 2nd formal release candidate for 2.4.0 + + -- Michael R. Crusoe <[email protected]> Tue, 30 Jan 2018 03:00:53 -0800 + + seqan2 (2.4.0~rc0+dfsg-1) experimental; urgency=medium + + * Testing upstream's formal release candidate + + -- Michael R. Crusoe <[email protected]> Fri, 26 Jan 2018 10:14:15 -0800 + + seqan2 (2.3.2.001platform-issues10-6f85721+dfsg-2) experimental; urgency=medium + + * enable asyncio on all archs as a test + * disable parallel building on powerpcspe + + -- Michael R. Crusoe <[email protected]> Thu, 04 Jan 2018 05:11:43 -0800 + + seqan2 (2.3.2.001platform-issues10-6f85721+dfsg-1) experimental; urgency=medium + + * Hopefully final update from upstream :-) + + -- Michael R. Crusoe <[email protected]> Wed, 03 Jan 2018 09:27:33 -0800 + + seqan2 (2.3.2.000platform-issues9-028fd79+dfsg-1) experimental; urgency=medium + + * Another update from upstream + * debian/rules: build flags simplification: + - use DEB_*_MAINT_APPEND + - pass -DNDEBUG -O3 as per upstream + - drop -DSEQAN_BUILD_SYSTEM=DEVELOP as that is the default + + -- Michael R. Crusoe <[email protected]> Fri, 22 Dec 2017 00:03:51 -0800 + + seqan2 (2.3.2.000platform-issues8-6f85721+dfsg-2) experimental; urgency=medium + + * Force rebuild + + -- Michael R. Crusoe <[email protected]> Thu, 14 Dec 2017 01:51:28 -0800 + + seqan2 (2.3.2.000platform-issues8-6f85721+dfsg-1) experimental; urgency=medium + + * Another update from upstream + + -- Michael R. Crusoe <[email protected]> Fri, 08 Dec 2017 04:41:18 -0800 + + seqan2 (2.3.2.000platform-issues7-41f58c3+dfsg-2) experimental; urgency=medium + + [ Andreas Tille ] + * Work around missing dir in indep-only builds + Closes: #882169 + + [ Michael R. Crusoe ] + * Cleanup from not pushing my changes + + -- Michael R. Crusoe <[email protected]> Wed, 06 Dec 2017 05:28:59 -0800 + + seqan2 (2.3.2.000platform-issues7-41f58c3+dfsg-1) experimental; urgency=medium + + * Another update from upstream + + -- Michael R. Crusoe <[email protected]> Tue, 21 Nov 2017 22:19:27 -0800 + + seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-3) experimental; urgency=medium + + * Typo fix + + -- Michael R. Crusoe <[email protected]> Sat, 18 Nov 2017 06:19:44 -0800 + + seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-2) experimental; urgency=medium + + * Now try -O3 everywhere + * Remove the sparc64 test code + * Delete symlinks for apps that are skipped for a particular architecture + + -- Michael R. Crusoe <[email protected]> Sat, 18 Nov 2017 04:50:55 -0800 + + seqan2 (2.3.2.000platform-issues6-9cf5a69+dfsg-1) experimental; urgency=medium + + * Skip yara on kfreebsd-i386 + * Try out -O2 on archs that had been previously -O1 + * Fix typo in bam2roi help text + * From upstream: another round of changes for the problems that affect + all big endian. + + -- Michael R. Crusoe <[email protected]> Sat, 11 Nov 2017 05:44:36 -0800 + + seqan2 (2.3.2.000platform-issues5-86390dc+dfsg-1) experimental; urgency=medium + + * Another update from upstream including a tweak to sparc64 + + -- Michael R. Crusoe <[email protected]> Wed, 08 Nov 2017 07:03:25 -0800 + + seqan2 (2.3.2.000platform-issues4-fba8744+dfsg-1) experimental; urgency=medium + + * Another refresh from upstream's branch + * Skip yara on armel, as well. + * d/control: declare seqan2 can be built without root, R³:no. + + -- Michael R. Crusoe <[email protected]> Mon, 06 Nov 2017 12:15:11 -0800 + + seqan2 (2.3.2.000platform-issues3-1d438c8+dfsg-2) experimental; urgency=medium + + * Skip yara on armhf & sh4. + * Disable parallel building on armel + + -- Michael R. Crusoe <[email protected]> Sat, 04 Nov 2017 02:09:12 -0700 + + seqan2 (2.3.2.000platform-issues3-1d438c8+dfsg-1) experimental; urgency=medium + + * require tests to pass everywhere + * skip the razers{3,} and yara apps on mips{el,} + * restore parallel build blocking only for armhf, sh4, and kfreebsd* + * Another refresh from upstream, this time focusing on bam files + + -- Michael R. Crusoe <[email protected]> Thu, 02 Nov 2017 11:41:21 -0700 + + seqan2 (2.3.2.000platform-issues2-206d1f7+dfsg-1) experimental; urgency=medium + + * Typo for CXXFLAGS: -O1 instead of -01 + * Another refresh from upstream in response to errors discovered via the + Debian build machines. + + -- Michael R. Crusoe <[email protected]> Thu, 26 Oct 2017 08:48:11 -0700 + + seqan2 (2.3.2.000platform-issues1-66a8baf+dfsg-1) experimental; urgency=medium + + * Refresh from upstream with additional fixes + + -- Michael R. Crusoe <[email protected]> Wed, 25 Oct 2017 04:08:29 -0700 + + seqan2 (2.3.2.000platform-issues0-8ae7bc0+dfsg1-1) experimental; urgency=medium + + * Patch for mips64el from [email protected] (Closes: #878933) + * Temporarily enable all archs again + * Upstream source is pre-2.4.0, remove patches that they have merged: + short-description, spelling + * Cleaned up per-arch settings in debian/rules + + -- Michael R. Crusoe <[email protected]> Mon, 23 Oct 2017 09:58:43 -0700 + +seqan2 (2.3.2+dfsg2-4) unstable; urgency=medium + + * Work around missing dir in indep-only builds + Closes: #882169 + * d/rules: drop --parallel which is redundant for debhelper 10 + * Do not generate manpages in arch indep builds (as done in + experimental branch) + + -- Andreas Tille <[email protected]> Wed, 06 Dec 2017 11:11:59 +0100 + +seqan2 (2.3.2+dfsg2-3) unstable; urgency=medium + + * Patch for mips64el from [email protected] (Closes: #878933) + * Cleaned up per-arch settings in debian/rules + * Disable parallel building on sh4 + + -- Michael R. Crusoe <[email protected]> Tue, 24 Oct 2017 04:56:12 -0700 + seqan2 (2.3.2+dfsg2-2) unstable; urgency=medium * As per upstream, disable async-io for many platforms -- 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
