[med-svn] [blasr] branch upstream updated (317d7eb -> afe0a9b)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository blasr.

      from  317d7eb   Imported Upstream version 5.3
       new  afe0a9b   Imported Upstream version 5.3+0

The 1 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:
 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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