[med-svn] [diamond-aligner] branch upstream updated (e37193d -> baec593)

[Andreas Tille]

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

      from  e37193d   New upstream version 0.9.8+dfsg
       new  baec593   New upstream version 0.9.10+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                                     |   4 +
 README.rst                                         |   2 +-
 build_simple.sh                                    |   4 +
 src/ChangeLog                                      |  14 +-
 src/align/align.cpp                                | 288 ++++-----------------
 src/align/align.h                                  |  64 +----
 src/align/align_queries.h                          |  67 -----
 src/align/align_target.cpp                         |   4 +
 src/align/query_mapper.cpp                         | 133 +++++-----
 src/align/query_mapper.h                           |  16 ++
 src/basic/basic.cpp                                |   4 +-
 src/basic/config.cpp                               |  28 +-
 src/basic/config.h                                 |   6 +-
 src/basic/const.h                                  |   2 +-
 src/basic/hssp.cpp                                 |  30 ++-
 src/basic/match.h                                  |   2 +
 src/basic/sequence.h                               |   9 +-
 src/basic/value.h                                  |   2 +-
 src/data/load_seqs.h                               |  12 +-
 src/data/reference.cpp                             |  22 ++
 src/data/reference.h                               |   9 +-
 src/data/taxonomy.cpp                              |  81 +++++-
 src/data/taxonomy.h                                |  15 ++
 src/dp/dp.h                                        |   7 +-
 src/dp/swipe.cpp                                   |   2 +-
 src/extra/match_file.h                             |   1 +
 src/output/blast_pairwise_format.cpp               |   5 +-
 src/output/blast_tab_format.cpp                    |   8 +-
 src/output/join_blocks.cpp                         |  51 +++-
 src/output/output.h                                |  39 ++-
 src/output/output_format.cpp                       |  25 +-
 src/output/output_format.h                         |  69 ++++-
 src/output/output_sink.cpp                         |  86 ++++++
 src/output/sam_format.cpp                          |   2 +-
 src/{util/system_c.h => output/target_culling.cpp} |  14 +-
 src/output/target_culling.h                        |  73 ++++++
 src/output/taxon_format.cpp                        |  51 ++++
 src/output/{view.h => view.cpp}                    |  67 ++---
 src/run/double_indexed.cpp                         |  10 +-
 src/run/main.cpp                                   |   7 +-
 src/run/tools.cpp                                  |   6 +-
 src/util/log_stream.h                              |   5 +
 src/util/{high_res_timer.h => queue.h}             |  62 ++---
 43 files changed, 825 insertions(+), 583 deletions(-)
 delete mode 100644 src/align/align_queries.h
 create mode 100644 src/output/output_sink.cpp
 copy src/{util/system_c.h => output/target_culling.cpp} (80%)
 create mode 100644 src/output/target_culling.h
 create mode 100644 src/output/taxon_format.cpp
 rename src/output/{view.h => view.cpp} (73%)
 copy src/util/{high_res_timer.h => queue.h} (62%)

-- 
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