[med-svn] [diamond-aligner] 03/07: Merge tag 'upstream/0.8.34+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository diamond-aligner.

commit 75907dcc63a86b69d28fc081c97550df66921323
Merge: f798f44 982daa6
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jan 25 21:19:35 2017 +0100

    Merge tag 'upstream/0.8.34+dfsg'
    
    Upstream version 0.8.34+dfsg

 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/{basic/const.h => extra/extra.h} |  33 +---
 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, 772 insertions(+), 299 deletions(-)

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