[med-svn] [pbdagcon] branch upstream updated (d20cc22 -> 7b1ae4f)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository pbdagcon.

      from  d20cc22   Imported Upstream version 0~20151114+git1d12e13+ds
       new  7b1ae4f   Imported Upstream version 0~20160325+ds

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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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 ++++
 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 +
 42 files changed, 913 insertions(+), 6682 deletions(-)
 copy src/cpp/pbdagcon_wf.sh => LICENSE (60%)
 mode change 100755 => 100644
 delete mode 100755 Makefile
 create mode 100755 configure.py
 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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