[med-svn] [blasr] branch master updated (cf7cb6e -> c6a674f)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch master
in repository blasr.

      from  cf7cb6e   releasing package blasr version 5.3-2
       new  afe0a9b   Imported Upstream version 5.3+0
       new  60139c3   Merge tag 'upstream/5.3+0'
       new  1920d57   Refresh patches
       new  c6a674f   releasing package blasr version 5.3+0-1

The 4 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 +-
 debian/changelog                            |  7 ++++
 debian/patches/cmake-utils.patch            |  4 +--
 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 +--
 29 files changed, 219 insertions(+), 85 deletions(-)

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