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commit b8aaf16a980797cdde23c968e068d0d407ddb5f6 Merge: 11817b4 9690aa9 Author: Afif Elghraoui <[email protected]> Date: Sun Jul 24 16:25:29 2016 -0700 Merge tag 'upstream/5.2' Upstream version 5.2 .gitignore | 9 + Blasr.cpp | 260 ++--- LICENSE | 34 + README.INSTALL.md | 24 +- configure.py | 10 +- cram.mk | 34 + ctest/.gitignore | 1 + ctest/bamConcordant.t | 33 + ctest/cigarAdjecentIndels.t | 22 + ctest/concordant.t | 7 +- ctest/dataset.t | 64 ++ ctest/deterministic.t | 47 + ctest/filtercriteria.t | 2 +- ctest/open_fail.t | 2 +- ctest/setup.sh | 7 +- ctest/unaligned.t | 25 + ctest/useccsallBestN1.t | 4 +- extrautils/BasH5Simulator.cpp | 524 ---------- extrautils/CCSH5ToBam.cpp | 135 --- extrautils/SimpleShredder.cpp | 2 +- extrautils/ctest/alchemy.t | 20 - extrautils/ctest/ccsh5tobam.t | 10 - extrautils/ctest/printTupleCountTable.t | 2 +- extrautils/makefile | 12 +- {include => iblasr}/BlasrAlign.hpp | 39 +- {include => iblasr}/BlasrAlignImpl.hpp | 157 ++- iblasr/BlasrHeaders.h | 113 +++ iblasr/BlasrMiscs.hpp | 62 ++ {include => iblasr}/BlasrMiscsImpl.hpp | 100 +- {include => iblasr}/BlasrUtils.hpp | 50 +- {include => iblasr}/BlasrUtilsImpl.hpp | 100 +- {include => iblasr}/MappingBuffers.hpp | 52 +- {include => iblasr}/MappingIPC.h | 30 +- {include => iblasr}/MappingParameters.h | 89 +- {include => iblasr}/MappingSemaphores.h | 15 +- {include => iblasr}/ReadAlignments.hpp | 45 +- {include => iblasr}/RegisterBlasrOptions.h | 402 ++++---- {include => iblasr}/RegisterFilterOptions.h | 41 +- include/BlasrHeaders.h | 149 --- include/BlasrMiscs.hpp | 100 -- makefile | 36 +- rules.mk | 9 +- sub.mk | 9 + utils/.gitignore | 2 + utils/LoadPulses.cpp | 145 ++- utils/PulseToFasta.cpp | 37 +- utils/SAWriter.cpp | 358 +++---- utils/SDPMatcher.cpp | 39 +- utils/SamFilter.cpp | 54 +- utils/SamToCmpH5.cpp | 29 +- utils/SamToM4.cpp | 26 +- utils/ToAfg.cpp | 42 +- utils/bam2bax/BUILD.txt | 48 + utils/bam2bax/CMakeLists.txt | 133 +++ utils/bam2bax/README.md | 11 + utils/bam2bax/makefile | 29 + utils/bam2bax/src/Bam2Bax.cpp | 29 + utils/bam2bax/src/Bam2Bax.h | 13 + utils/bam2bax/src/Bam2BaxConverter.h | 38 + utils/bam2bax/src/Bam2BaxConverterImpl.hpp | 71 ++ utils/bam2bax/src/Bam2BaxInternal.h | 78 ++ utils/bam2bax/src/Bam2BaxMain.cpp | 75 ++ utils/bam2bax/src/Bam2PlxMain.cpp | 65 ++ utils/bam2bax/src/CMakeLists.txt | 79 ++ utils/bam2bax/src/Converter.cpp | 146 +++ utils/bam2bax/src/Converter.h | 77 ++ utils/bam2bax/src/MetadataWriter.cpp | 42 + utils/bam2bax/src/MetadataWriter.h | 38 + utils/bam2bax/src/OptionParser.cpp | 562 +++++++++++ utils/bam2bax/src/OptionParser.h | 306 ++++++ utils/bam2bax/src/RegionTypeAdapter.h | 129 +++ utils/bam2bax/src/RegionsAdapter.h | 118 +++ utils/bam2bax/src/Settings.cpp | 232 +++++ utils/bam2bax/src/Settings.h | 80 ++ utils/bam2bax/tests/CMakeLists.txt | 93 ++ utils/bam2bax/tests/cram/bam2bax.t | 86 ++ utils/bam2bax/tests/cram/bam2plx.t | 230 +++++ ...4852550000001823085912221377_s1_X0.1.scraps.bam | Bin 0 -> 644642 bytes ...52550000001823085912221377_s1_X0.1.subreads.bam | Bin 0 -> 220556 bytes utils/bam2bax/tests/data/tiny.scraps.sam | 18 + utils/bam2bax/tests/data/tiny.subreads.sam | 27 + .../bam2bax/tests/data/tiny_bam2plx.polymerase.sam | 4 + utils/bam2bax/tests/example/end-to-end.sh | 66 ++ utils/bam2bax/tests/files.cmake | 64 ++ .../tests/resequencing/bam2bax_resequencing.py | 179 ++++ utils/bam2bax/tests/resequencing/one_bax_test.sh | 5 + utils/bam2bax/tests/resequencing/settings.xml | 201 ++++ utils/bam2bax/tests/resequencing/tiny_test.sh | 5 + utils/bam2bax/tests/src/TestConstants.h | 195 ++++ utils/bam2bax/tests/src/TestData.h.in | 18 + utils/bam2bax/tests/src/TestUtils.cpp | 42 + utils/bam2bax/tests/src/TestUtils.h | 13 + utils/bam2bax/tests/src/test.cpp | 23 + utils/bam2bax/tests/src/test_Bam2BaxConverter.cpp | 94 ++ .../bam2bax/tests/src/test_HDFBaseCallsWriter.cpp | 56 ++ utils/bam2bax/tests/src/test_HDFBaxWriter.cpp | 100 ++ utils/bam2bax/tests/src/test_HDFScanDataWriter.cpp | 76 ++ .../bam2bax/tests/src/test_HDFZMWMetricsWriter.cpp | 51 + utils/bam2bax/tests/src/test_HDFZMWWriter.cpp | 40 + utils/bax2bam/BUILD.txt | 10 + utils/bax2bam/CMakeLists.txt | 128 +++ utils/bax2bam/README.md | 62 ++ utils/bax2bam/makefile | 29 + utils/bax2bam/src/Bax2Bam.cpp | 191 ++++ utils/bax2bam/src/Bax2Bam.h | 13 + utils/bax2bam/src/CMakeLists.txt | 57 ++ utils/bax2bam/src/CcsConverter.cpp | 117 +++ utils/bax2bam/src/CcsConverter.h | 47 + utils/bax2bam/src/ConverterBase.h | 1019 ++++++++++++++++++++ utils/bax2bam/src/HqRegionConverter.cpp | 192 ++++ utils/bax2bam/src/HqRegionConverter.h | 26 + utils/bax2bam/src/IConverter.cpp | 85 ++ utils/bax2bam/src/IConverter.h | 53 + utils/bax2bam/src/OptionParser.cpp | 562 +++++++++++ utils/bax2bam/src/OptionParser.h | 306 ++++++ utils/bax2bam/src/PolymeraseReadConverter.cpp | 60 ++ utils/bax2bam/src/PolymeraseReadConverter.h | 26 + utils/bax2bam/src/Settings.cpp | 261 +++++ utils/bax2bam/src/Settings.h | 87 ++ utils/bax2bam/src/SubreadConverter.cpp | 395 ++++++++ utils/bax2bam/src/SubreadConverter.h | 26 + utils/bax2bam/src/main.cpp | 118 +++ utils/bax2bam/tests/CMakeLists.txt | 88 ++ utils/bax2bam/tests/bax2bam.t | 7 + utils/bax2bam/tests/files.cmake | 52 + utils/bax2bam/tests/src/TestData.h.in | 17 + utils/bax2bam/tests/src/TestUtils.cpp | 43 + utils/bax2bam/tests/src/TestUtils.h | 13 + utils/bax2bam/tests/src/test_ccs.cpp | 219 +++++ utils/bax2bam/tests/src/test_common.cpp | 16 + utils/bax2bam/tests/src/test_hqregions.cpp | 421 ++++++++ utils/bax2bam/tests/src/test_polymerase.cpp | 236 +++++ utils/bax2bam/tests/src/test_subreads.cpp | 410 ++++++++ .../gtest/.deps/test_fused_gtest_test-gtest-all.Po | 1 + .../.deps/test_fused_gtest_test-gtest_main.Po | 1 + .../bax2bam/third-party/gtest-1.7.0/lib/.dirstamp | 0 .../gtest-1.7.0/samples/.deps/.dirstamp | 0 .../gtest-1.7.0/samples/.deps/sample1.Plo | 3 + .../gtest-1.7.0/samples/.deps/sample10_unittest.Po | 1 + .../gtest-1.7.0/samples/.deps/sample1_unittest.Po | 1 + .../gtest-1.7.0/samples/.deps/sample2.Plo | 29 + .../gtest-1.7.0/samples/.deps/sample4.Plo | 48 + .../samples/.deps/test_fused_gtest_test-sample1.Po | 1 + .../test_fused_gtest_test-sample1_unittest.Po | 1 + .../third-party/gtest-1.7.0/samples/.dirstamp | 0 .../third-party/gtest-1.7.0/src/.deps/.dirstamp | 0 .../gtest-1.7.0/src/.deps/gtest-all.Plo | 617 ++++++++++++ .../gtest-1.7.0/src/.deps/gtest_main.Plo | 460 +++++++++ .../bax2bam/third-party/gtest-1.7.0/src/.dirstamp | 0 .../gtest-1.7.0/test/.deps/gtest_all_test.Po | 1 + utils/ctest/.gitignore | 1 + utils/makefile | 22 +- 152 files changed, 12135 insertions(+), 2149 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
