[med-svn] [diamond-aligner] branch master updated (c373427 -> d2d3a75)
Andreas Tille
tille at debian.org
Mon Jun 19 06:43:49 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository diamond-aligner.
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
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