This is an automated email from the git hooks/post-receive script. tille pushed a change to branch upstream in repository diamond-aligner.
from b84b9ff New upstream version 0.8.35+dfsg new e37193d New upstream version 0.9.8+dfsg The 1 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 +- 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 +++++- 147 files changed, 8059 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 _______________________________________________ debian-med-commit mailing list 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