[med-svn] [diamond-aligner] branch master updated (d2d3a75 -> eaa0274)

[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  d2d3a75   New upstream version
       new  baec593   New upstream version 0.9.10+dfsg
       new  c5e9593   Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg'
       new  aa9a12b   New upstream version
       new  c87ab56   Force the symbol with c++ explicit function template instantiation for the latter prototype instead of relying on implicit instantiation Upload and see, whether this will help to fix bug   #865132
       new  2c10a77   Standards-Version: 4.1.0 (no changes needed)
       new  608f5e6   Do not parse d/changelog
       new  eaa0274   Fix typo in d/rules and upload to unstable

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                                     |   4 +
 README.rst                                         |   2 +-
 build_simple.sh                                    |   4 +
 debian/changelog                                   |  10 +
 debian/control                                     |   2 +-
 debian/patches/avoid_unwanted_optimisation.patch   |  17 ++
 debian/patches/series                              |   1 +
 debian/rules                                       |  14 +-
 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 ++---
 48 files changed, 861 insertions(+), 591 deletions(-)
 create mode 100644 debian/patches/avoid_unwanted_optimisation.patch
 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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