[med-svn] [blasr] 08/13: Merge tag 'upstream/5.3'
Afif Elghraoui
afif at moszumanska.debian.org
Mon Oct 24 01:24:35 UTC 2016
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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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