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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
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