[med-svn] [diamond-aligner] branch master updated (68c550f -> 1ae1467)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

      from  68c550f   Add missing copyright
       new  f798f44   Remove PDF manual since it seems it was not generated from README
       new  982daa6   New upstream version 0.8.34+dfsg
       new  75907dc   Merge tag 'upstream/0.8.34+dfsg'
       new  6f5813f   Add missing license
       new  07ba80a   New upstream version
       new  eb27031   PDF was removed
       new  1ae1467   Drop -march=native flag

The 7 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 +
 debian/changelog                            |   9 +-
 debian/copyright                            |  21 +-
 debian/docs                                 |   1 -
 debian/patches/drop_march_native_flag.patch |  21 ++
 debian/patches/series                       |   1 +
 debian/watch                                |   3 +-
 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 +-
 54 files changed, 825 insertions(+), 289 deletions(-)
 create mode 100644 debian/patches/drop_march_native_flag.patch
 create mode 100644 debian/patches/series
 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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