[med-svn] [blasr] 06/12: Merge tag 'upstream/0_20151014+git8e668be'

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository blasr.

commit 74cd6870abcc537b7d85e59b065bea4008ed2b8b
Merge: 7181937 b282ecd
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Dec 13 12:41:39 2015 -0800

    Merge tag 'upstream/0_20151014+git8e668be'
    
    Upstream version 0~20151014+git8e668be

 Blasr.cpp                                          | 4351 ++++----------------
 MappingSemaphores.h                                |   45 -
 README.INSTALL.md                                  |   18 +-
 configure.py                                       |   21 +-
 ctest/affineAlign.t                                |    2 +-
 include/BlasrAlign.hpp                             |  122 +
 include/BlasrAlignImpl.hpp                         | 1564 +++++++
 include/BlasrHeaders.h                             |  149 +
 include/BlasrMiscs.hpp                             |  100 +
 include/BlasrMiscsImpl.hpp                         |  223 +
 include/BlasrUtils.hpp                             |  199 +
 include/BlasrUtilsImpl.hpp                         | 1225 ++++++
 include/MappingBuffers.hpp                         |  116 +
 MappingIPC.h => include/MappingIPC.h               |    4 +-
 MappingParameters.h => include/MappingParameters.h |   40 +-
 include/MappingSemaphores.h                        |   45 +
 include/ReadAlignments.hpp                         |  199 +
 .../RegisterBlasrOptions.h                         |   62 +-
 .../RegisterFilterOptions.h                        |   30 +-
 makefile                                           |    2 +
 rules.mk                                           |    3 +
 utils/PulseToFasta.cpp                             |  106 +-
 utils/SamFilter.cpp                                |    2 +-
 utils/ToAfg.cpp                                    |   15 +-
 24 files changed, 4794 insertions(+), 3849 deletions(-)

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