[med-svn] [diamond-aligner] branch upstream updated (d6d7781 -> 982daa6)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository diamond-aligner.

      from  d6d7781   New upstream version 0.8.31
       new  982daa6   New upstream version 0.8.34+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                     |   1 +
 README.rst                         |   4 +-
 build_simple.sh                    |   1 +
 diamond_manual.pdf                 | Bin 92606 -> 0 bytes
 src/ChangeLog                      |  11 ++
 src/align/align.cpp                |  14 +-
 src/align/query_mapper.cpp         |  16 +-
 src/basic/basic.cpp                |   2 +-
 src/basic/config.cpp               |  33 +++-
 src/basic/config.h                 |   9 +-
 src/basic/const.h                  |   2 +-
 src/basic/hssp.cpp                 |   2 +
 src/basic/reduction.h              |   1 +
 src/basic/shape.h                  |  55 ++++++-
 src/basic/statistics.h             |   5 +-
 src/basic/value.h                  |   7 +
 src/data/frequent_seeds.h          |   2 +-
 src/data/load_seqs.h               |  16 +-
 src/data/reference.h               |  10 +-
 src/data/string_set.h              |   7 +
 src/dp/dp.h                        |   1 +
 src/dp/dp_matrix.h                 |   2 +
 src/dp/floating_sw.cpp             |   6 +-
 src/dp/growing_buffer.h            |   1 +
 src/dp/padded_banded_sw.cpp        |   2 +
 src/{run/tools.h => extra/extra.h} |  20 +--
 src/extra/model_sim.cpp            |  11 +-
 src/extra/opt.cpp                  | 307 +++++++++++++++++++++++++++++++++++++
 src/output/daa_file.h              |   1 +
 src/output/join_blocks.cpp         |  25 ++-
 src/output/output.h                |  11 +-
 src/run/benchmark.cpp              |  62 ++++++--
 src/run/double_indexed.cpp         |  11 +-
 src/run/main.cpp                   |   4 +
 src/search/align_range.h           |  66 ++++++++
 src/search/search.cpp              |   3 -
 src/search/setup.cpp               |   7 +-
 src/search/sse_dist.h              | 133 ----------------
 src/search/stage2.cpp              |  43 +++++-
 src/search/trace_pt_buffer.h       |   7 +-
 src/util/async_buffer.h            |  68 ++++----
 src/util/binary_file.h             |   3 +-
 src/util/double_buffer.h           |   1 +
 src/util/log_stream.h              |  20 ++-
 src/util/system.h                  |  28 ++++
 src/util/tinythread.cpp            |   2 +
 src/util/util.cpp                  |   1 +
 src/util/util.h                    |  14 +-
 48 files changed, 773 insertions(+), 285 deletions(-)
 delete mode 100644 diamond_manual.pdf
 copy src/{run/tools.h => extra/extra.h} (84%)
 create mode 100644 src/extra/opt.cpp

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