[med-svn] [diamond-aligner] 02/03: Merge tag 'upstream/0.9.8+dfsg'
Andreas Tille
tille at debian.org
Mon Jun 19 06:43:49 UTC 2017
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tille pushed a commit to branch master
in repository diamond-aligner.
commit 75c0c85b4140a788122afaa4a2faf6fe4066f0cd
Merge: c373427 e37193d
Author: Andreas Tille <tille at debian.org>
Date: Mon Jun 19 08:14:09 2017 +0200
Merge tag 'upstream/0.9.8+dfsg'
Upstream version 0.9.8+dfsg
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(-)
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