[med-svn] [pbdagcon] branch master updated (7aa546f -> 90e5932)

[Afif Elghraoui]

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

afif pushed a change to branch master
in repository pbdagcon.

      from  7aa546f   releasing package pbdagcon version 0~20151114+git1d12e13+ds-3
       new  7b1ae4f   Imported Upstream version 0~20160325+ds
       new  81a615b   Merge tag 'upstream/0_20160325+ds'
       new  f8f7818   Do not use rpath for pbseqlib
       new  31669ba   Update patches
       new  3b309a6   d/rules: update for changes to build system and dependencies
       new  42116d3   Do not build dazcon for now (needs additional sources)
       new  892ceb9   d/copyright: Remove obsolete declarations
       new  90e5932   releasing package pbdagcon version 0~20160325+ds-1

The 8 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:
 .gitignore                                |    1 +
 .gitmodules                               |    8 +-
 .travis.yml                               |    4 +-
 src/cpp/pbdagcon_wf.sh => LICENSE         |   40 +-
 Makefile                                  |   48 -
 README.md                                 |   27 +-
 configure.py                              |  320 +++
 debian/TODO                               |    1 +
 debian/changelog                          |   12 +
 debian/control                            |    1 +
 debian/copyright                          |   28 -
 debian/lintian-overrides                  |    5 -
 debian/patches/compiler-flags.patch       |   30 +-
 debian/patches/dazcon.patch               |   16 +
 debian/patches/disable-dazcon-tests.patch |   16 -
 debian/patches/external-libs.patch        |   29 -
 debian/patches/gtest-directory.patch      |   90 -
 debian/patches/series                     |    4 +-
 debian/rules                              |   21 +-
 makefile                                  |   45 +
 src/cpp/Alignment.cpp                     |  123 +-
 src/cpp/Alignment.hpp                     |   55 +-
 src/cpp/AlnGraphBoost.cpp                 |  108 +-
 src/cpp/AlnGraphBoost.hpp                 |   67 +-
 src/cpp/AlnProvider.hpp                   |   47 +-
 src/cpp/BlasrM5AlnProvider.cpp            |   40 +-
 src/cpp/BlasrM5AlnProvider.hpp            |   55 +-
 src/cpp/BoundedBuffer.hpp                 |   53 +-
 src/cpp/DB.c                              | 1106 ---------
 src/cpp/DB.h                              |  357 ---
 src/cpp/DazAlnProvider.cpp                |   79 +-
 src/cpp/DazAlnProvider.hpp                |   62 +-
 src/cpp/Makefile                          |   38 -
 src/cpp/ProgramOpts.hpp                   |    5 +-
 src/cpp/SimpleAligner.cpp                 |   40 +-
 src/cpp/SimpleAligner.hpp                 |   42 +-
 src/cpp/align.c                           | 3805 -----------------------------
 src/cpp/align.h                           |  331 ---
 src/cpp/boost.mk                          |   18 -
 src/cpp/dazcon.cpp                        |   78 +-
 src/cpp/main.cpp                          |   88 +-
 src/cpp/makefile                          |   76 +
 src/cpp/pbdagcon_wf.sh                    |   39 -
 src/cpp/pbi.mk                            |   22 -
 src/q-sense.py                            |   39 -
 test/cpp/.gitignore                       |    2 +
 test/cpp/AlignmentTest.cpp                |   89 +-
 test/cpp/AlnGraphBoostTest.cpp            |    9 +-
 test/cpp/Makefile                         |   77 -
 test/cpp/TargetHitTest.cpp                |   14 +-
 test/cpp/TargetTest.cpp                   |    4 +-
 test/cpp/gtest.mk                         |   10 -
 test/cpp/makefile                         |  117 +
 travis.sh                                 |    7 +
 54 files changed, 968 insertions(+), 6880 deletions(-)
 copy src/cpp/pbdagcon_wf.sh => LICENSE (60%)
 mode change 100755 => 100644
 delete mode 100755 Makefile
 create mode 100755 configure.py
 create mode 100644 debian/TODO
 delete mode 100644 debian/lintian-overrides
 create mode 100644 debian/patches/dazcon.patch
 delete mode 100644 debian/patches/disable-dazcon-tests.patch
 delete mode 100644 debian/patches/external-libs.patch
 delete mode 100644 debian/patches/gtest-directory.patch
 create mode 100755 makefile
 delete mode 100644 src/cpp/DB.c
 delete mode 100644 src/cpp/DB.h
 delete mode 100644 src/cpp/Makefile
 delete mode 100644 src/cpp/align.c
 delete mode 100644 src/cpp/align.h
 delete mode 100644 src/cpp/boost.mk
 create mode 100644 src/cpp/makefile
 delete mode 100644 src/cpp/pbi.mk
 create mode 100644 test/cpp/.gitignore
 delete mode 100644 test/cpp/Makefile
 delete mode 100644 test/cpp/gtest.mk
 create mode 100644 test/cpp/makefile
 create mode 100755 travis.sh

-- 
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