[med-svn] [diamond-aligner] 02/07: Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg'

[Andreas Tille]

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

commit c5e9593e49b8ca59317dc3ea11de82ab284f723e
Merge: d2d3a75 baec593
Author: Andreas Tille <tille at debian.org>
Date:   Mon Sep 18 13:30:40 2017 +0200

    Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg'
    
    with Debian dir d7e6526cc3f25884323dd55b00e1052088978fa5

 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/{basic/const.h => output/target_culling.cpp} |  30 +--
 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/{basic/const.h => util/queue.h}              |  59 +++--
 43 files changed, 830 insertions(+), 591 deletions(-)

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