[med-svn] [blasr] 02/04: Merge tag 'upstream/5.3+0'

[Afif Elghraoui]

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afif pushed a commit to branch master
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commit 60139c32ce6dfdc00f58acf46ef8d0e46e4b2799
Merge: cf7cb6e afe0a9b
Author: Afif Elghraoui <afif at debian.org>
Date:   Fri Dec 23 16:51:51 2016 -0800

    Merge tag 'upstream/5.3+0'
    
    Upstream version 5.3+0

 cram.mk                                     | 21 +++++++----
 ctest/aggressiveIntervalCut.t               |  4 +--
 ctest/concordant.t                          | 39 ++++++++++-----------
 ctest/ecoli.t                               |  9 +++--
 ctest/fastMaxInterval.t                     |  4 +--
 ctest/multipart.t                           |  4 +--
 ctest/noSplitSubreads.t                     | 34 ++++++++++++++++++
 ctest/useccsallBestN1.t                     |  2 +-
 iblasr/MappingParameters.h                  | 26 +++++++++++++-
 iblasr/RegisterBlasrOptions.h               | 11 +++---
 makefile                                    |  4 +++
 utils/bam2bax/BUILD.txt                     | 54 ++++++++++++++++++++---------
 utils/bam2bax/CMakeLists.txt                | 10 ++++--
 utils/bam2bax/makefile                      | 22 ++++++++++++
 utils/bam2bax/src/CMakeLists.txt            |  2 ++
 utils/bam2bax/tests/CMakeLists.txt          |  1 +
 utils/bax2bam/CMakeLists.txt                |  9 ++++-
 utils/bax2bam/makefile                      |  4 +++
 utils/bax2bam/src/CMakeLists.txt            |  1 +
 utils/bax2bam/src/IConverter.cpp            |  7 ----
 utils/bax2bam/src/main.cpp                  |  2 +-
 utils/bax2bam/tests/CMakeLists.txt          |  1 +
 utils/bax2bam/tests/src/TestData.h.in       |  2 ++
 utils/bax2bam/tests/src/test_ccs.cpp        |  4 +--
 utils/bax2bam/tests/src/test_hqregions.cpp  |  8 ++---
 utils/bax2bam/tests/src/test_polymerase.cpp |  4 +--
 utils/bax2bam/tests/src/test_subreads.cpp   |  4 +--
 27 files changed, 210 insertions(+), 83 deletions(-)

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