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commit 0fc2023e4fc3fc10fea40c4e5cb56f5bdebfb40d Merge: 3a12f90 317d7eb Author: Afif Elghraoui <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
