[med-svn] [blasr] 08/13: Merge tag 'upstream/5.3'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository blasr.

commit 0fc2023e4fc3fc10fea40c4e5cb56f5bdebfb40d
Merge: 3a12f90 317d7eb
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Oct 23 15:45:02 2016 -0700

    Merge tag 'upstream/5.3'
    
    Upstream version 5.3

 Blasr.cpp                                   | 36 ++++++++++++---
 cram.mk                                     | 11 +++--
 ctest/affineAlign.t                         |  6 +--
 ctest/aggressiveIntervalCut.t               |  4 +-
 ctest/alignScore.t                          |  2 +-
 ctest/bamConcordant.t                       |  6 +--
 ctest/bamIn.t                               | 39 ++--------------
 ctest/bamOut.t                              |  4 +-
 ctest/bug25328.t                            |  2 +-
 ctest/bug25741.t                            |  9 ----
 ctest/bug25766.t                            |  4 +-
 ctest/ccsH5.t                               |  4 +-
 ctest/cigarAdjecentIndels.t                 |  8 ++--
 ctest/concordant.t                          | 14 +++---
 ctest/dataset.t                             | 16 +++----
 ctest/deterministic.t                       |  6 +--
 ctest/ecoli.t                               | 10 ++--
 ctest/fastMaxInterval.t                     |  4 +-
 ctest/filtercriteria.t                      |  6 +--
 ctest/fofn.t                                |  4 +-
 ctest/hitpolicy.t                           | 18 ++++----
 ctest/holeNumbers.t                         |  4 +-
 ctest/m0-5.t                                | 10 ++--
 ctest/multipart.t                           |  2 +-
 ctest/noSplitSubreads.t                     |  6 +--
 ctest/samNM.t                               | 13 ------
 ctest/setup.sh                              |  3 +-
 ctest/unaligned.t                           |  4 +-
 ctest/useccsallBestN1.t                     |  5 +-
 ctest/useccsallLargeGenome.t                |  4 +-
 ctest/verbose.t                             |  2 +-
 iblasr/BlasrHeaders.h                       |  1 +
 iblasr/BlasrUtils.hpp                       |  7 +--
 iblasr/BlasrUtilsImpl.hpp                   | 11 +++--
 iblasr/MappingParameters.h                  | 49 ++++++++++++++++++--
 iblasr/RegisterBlasrOptions.h               | 10 ++--
 makefile                                    |  2 +-
 rules.mk                                    |  2 +-
 utils/SamFilter.cpp                         |  2 +-
 utils/bam2bax/makefile                      |  3 +-
 utils/bam2bax/src/Bam2BaxConverterImpl.hpp  | 14 ------
 utils/bam2bax/src/Bam2BaxMain.cpp           |  4 +-
 utils/bam2bax/src/Bam2PlxMain.cpp           |  4 +-
 utils/bam2bax/src/Converter.cpp             | 16 -------
 utils/bam2bax/src/Settings.cpp              | 12 +----
 utils/bam2bax/tests/cram/bam2bax.t          | 22 ++++-----
 utils/bam2bax/tests/cram/bam2plx.t          | 12 ++---
 utils/bax2bam/CMakeLists.txt                |  2 +
 utils/bax2bam/README.md                     |  4 +-
 utils/bax2bam/makefile                      |  5 +-
 utils/bax2bam/src/Bax2Bam.cpp               | 72 ++++++++++++++++++++++++++---
 utils/bax2bam/src/CMakeLists.txt            |  2 +
 utils/bax2bam/src/ConverterBase.h           | 16 ++++---
 utils/bax2bam/src/Settings.cpp              | 12 ++++-
 utils/bax2bam/src/Settings.h                |  4 ++
 utils/bax2bam/src/main.cpp                  | 15 +++++-
 utils/bax2bam/tests/CMakeLists.txt          |  1 +
 utils/bax2bam/tests/bax2bam.t               |  2 +-
 utils/bax2bam/tests/src/TestData.h.in       |  2 +-
 utils/bax2bam/tests/src/test_ccs.cpp        |  2 +-
 utils/bax2bam/tests/src/test_hqregions.cpp  | 13 +++---
 utils/bax2bam/tests/src/test_polymerase.cpp | 18 ++++----
 utils/bax2bam/tests/src/test_subreads.cpp   | 12 +++--
 utils/ctest/samFilter.t                     | 24 +++++-----
 64 files changed, 366 insertions(+), 277 deletions(-)

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