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from c373427 New upstream version build also on 32bit arch new e37193d New upstream version 0.9.8+dfsg new 75c0c85 Merge tag 'upstream/0.9.8+dfsg' new d2d3a75 New upstream version The 3 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: CMakeLists.txt | 14 +- LICENSE | 619 +++++++++++++++++++++++++ README.rst | 3 +- build_simple.sh | 16 +- debian/changelog | 6 + src/COPYING | 12 - src/ChangeLog | 53 +++ src/align/align.cpp | 194 +++++++- src/align/align.h | 91 +++- src/align/align_queries.h | 26 +- src/align/align_struct.h | 24 +- src/align/align_target.cpp | 259 ++++++++--- src/align/extend_ungapped.h | 24 +- src/align/match_func.h | 26 +- src/align/query_mapper.cpp | 109 +++-- src/align/query_mapper.h | 77 ++- src/basic/basic.cpp | 56 ++- src/basic/config.cpp | 153 +++--- src/basic/config.h | 63 ++- src/basic/const.h | 26 +- src/basic/hssp.cpp | 40 +- src/basic/masking.cpp | 94 ++++ src/basic/masking.h | 50 ++ src/basic/match.h | 75 ++- src/basic/packed_loc.h | 26 +- src/basic/packed_sequence.h | 25 +- src/basic/packed_transcript.h | 45 +- src/basic/reduction.h | 35 +- src/basic/score_matrix.cpp | 65 ++- src/basic/score_matrix.h | 46 +- src/basic/seed.h | 24 +- src/basic/seed_iterator.h | 97 +++- src/basic/sequence.h | 45 +- src/basic/shape.h | 58 ++- src/basic/shape_config.h | 30 +- src/basic/statistics.h | 77 +-- src/basic/translate.h | 26 +- src/basic/value.h | 24 +- src/data/count_approximate.cpp | 110 ----- src/data/frequent_seeds.cpp | 26 +- src/data/frequent_seeds.h | 29 +- src/data/index.cpp | 86 ---- src/data/index.h | 24 +- src/data/load_seqs.h | 71 +-- src/data/queries.cpp | 26 +- src/data/queries.h | 30 +- src/data/reference.cpp | 105 +++-- src/data/reference.h | 28 +- src/data/seed_histogram.cpp | 39 +- src/data/seed_histogram.h | 105 ++--- src/data/seed_set.cpp | 82 ++++ src/data/seed_set.h | 52 +++ src/data/sequence_set.h | 241 +++++----- src/data/sorted_list.cpp | 76 +++ src/data/sorted_list.h | 153 +++--- src/data/string_set.h | 38 +- src/data/taxonomy.cpp | 66 +++ src/data/taxonomy.h | 90 ++++ src/dp/banded_sw.cpp | 316 +++++++++++++ src/dp/comp_based_stats.cpp | 33 +- src/dp/diag_scores.cpp | 315 +++++++++++++ src/dp/dp.h | 416 +++++++++++++++-- src/dp/dp_matrix.h | 26 +- src/dp/floating_sw.cpp | 43 +- src/dp/floating_sw.h | 25 +- src/dp/greedy_align.cpp | 876 ++++++++++++++++++----------------- src/dp/growing_buffer.h | 25 +- src/dp/needleman_wunsch.cpp | 211 +++++++-- src/dp/padded_banded_sw.cpp | 24 +- src/dp/scalar_dp_matrix.h | 25 +- src/dp/scalar_traceback.h | 25 +- src/dp/score_profile.h | 30 +- src/dp/score_vector.h | 33 +- src/dp/smith_waterman.cpp | 24 +- src/dp/smith_waterman.h | 26 +- src/dp/swipe.cpp | 249 ++++++++++ src/dp/traceback.h | 28 +- src/dp/ungapped_align.cpp | 109 ++++- src/extra/blast_record.h | 18 + src/extra/compare.h | 18 + src/extra/extra.h | 24 +- src/extra/match_file.h | 19 + src/extra/model_sim.cpp | 24 +- src/extra/opt.cpp | 24 +- src/extra/roc.cpp | 25 +- src/lib/tantan/tantan.cc | 462 ++++++++++++++++++ src/lib/tantan/tantan.hh | 120 +++++ src/output/blast_pairwise_format.cpp | 37 +- src/output/blast_tab_format.cpp | 64 ++- src/output/daa_file.h | 24 +- src/output/daa_record.cpp | 29 +- src/output/daa_record.h | 24 +- src/output/daa_write.h | 38 +- src/output/join_blocks.cpp | 24 +- src/output/output.h | 36 +- src/output/output_file.h | 64 --- src/output/output_format.cpp | 90 +++- src/output/output_format.h | 72 ++- src/output/sam_format.cpp | 26 +- src/output/view.h | 49 +- src/run/benchmark.cpp | 356 ++++++++++++-- src/run/double_indexed.cpp | 184 +++++--- src/run/main.cpp | 43 +- src/run/mapper.cpp | 112 ----- src/run/tools.cpp | 62 ++- src/run/tools.h | 24 +- src/search/align_range.h | 26 +- src/search/collision.cpp | 34 +- src/search/collision.h | 24 +- src/search/hit_filter.h | 30 +- src/search/search.cpp | 24 +- src/search/search_query.cpp | 51 -- src/search/setup.cpp | 79 +++- src/search/sse_dist.h | 31 +- src/search/stage2.cpp | 63 +-- src/search/trace_pt_buffer.h | 26 +- src/util/async_buffer.h | 86 +++- src/util/binary_buffer.h | 25 +- src/util/binary_file.cpp | 355 ++++++++++++++ src/util/binary_file.h | 416 ++--------------- src/util/command_line_parser.cpp | 24 +- src/util/command_line_parser.h | 24 +- src/util/complexity_filter.h | 26 +- src/util/compressed_stream.cpp | 61 +-- src/util/compressed_stream.h | 26 +- src/util/direction.h | 26 +- src/util/double_buffer.h | 26 +- src/util/hash_function.h | 26 +- src/util/hash_table.h | 80 +++- src/util/high_res_timer.h | 61 +++ src/util/log_stream.h | 28 +- src/util/map.h | 30 +- src/util/merge_sort.h | 26 +- src/util/ptr_vector.h | 24 +- src/util/radix_sort.h | 24 +- src/util/seq_file_format.cpp | 24 +- src/util/seq_file_format.h | 26 +- src/util/simd.cpp | 60 +++ src/util/simd.h | 53 +-- src/util/system.h | 45 +- src/util/system_c.h | 18 + src/util/task_queue.h | 26 +- src/util/temp_file.h | 24 +- src/util/text_buffer.h | 62 ++- src/util/thread.h | 90 +++- src/util/tinythread.cpp | 301 ++++++------ src/util/util.cpp | 70 +-- src/util/util.h | 142 +++++- 148 files changed, 8065 insertions(+), 3819 deletions(-) create mode 100644 LICENSE delete mode 100644 src/COPYING create mode 100644 src/basic/masking.cpp create mode 100644 src/basic/masking.h delete mode 100644 src/data/count_approximate.cpp delete mode 100644 src/data/index.cpp create mode 100644 src/data/seed_set.cpp create mode 100644 src/data/seed_set.h create mode 100644 src/data/sorted_list.cpp create mode 100644 src/data/taxonomy.cpp create mode 100644 src/data/taxonomy.h create mode 100644 src/dp/banded_sw.cpp create mode 100644 src/dp/diag_scores.cpp create mode 100644 src/dp/swipe.cpp create mode 100644 src/lib/tantan/tantan.cc create mode 100644 src/lib/tantan/tantan.hh delete mode 100644 src/output/output_file.h delete mode 100644 src/run/mapper.cpp delete mode 100644 src/search/search_query.cpp create mode 100644 src/util/binary_file.cpp create mode 100644 src/util/high_res_timer.h create mode 100644 src/util/simd.cpp -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/diamond-aligner.git _______________________________________________ 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