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commit 0ea2ca61f850661dd7379a065f2d16f9a90f204d Merge: b32b993 ce58675 Author: Afif Elghraoui <[email protected]> Date: Mon Jul 4 15:18:42 2016 -0700 Merge tag 'upstream/0.5.0' Upstream version 0.5.0 .travis.yml | 64 + CHANGELOG.md | 248 +- CMakeLists.txt | 80 +- INSTALL.md | 115 +- LICENSE.txt | 34 + README.md | 29 + cmake/FindCSharp.cmake | 72 + cmake/FindDotNetFrameworkSdk.cmake | 29 + cmake/FindMono.cmake | 167 + cmake/FindR.cmake | 48 + cmake/PbbamTool.cmake | 23 + cmake/UseCSharp.cmake | 111 + cmake/UseDotNetFrameworkSdk.cmake | 16 + cmake/UseMono.cmake | 16 + docs/Doxyfile.in | 24 +- docs/Makefile | 168 + docs/examples/code/BarcodeQuery.txt | 17 + docs/examples/code/Compare.txt | 3 + docs/examples/code/Compare_AlignedEnd.txt | 2 + docs/examples/code/Compare_AlignedStart.txt | 2 + docs/examples/code/Compare_AlignedStrand.txt | 2 + docs/examples/code/Compare_BarcodeForward.txt | 2 + docs/examples/code/Compare_BarcodeQuality.txt | 2 + docs/examples/code/Compare_BarcodeReverse.txt | 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tests/src/R/tests/test_PolymeraseStitching.R | 427 ++ tests/src/TestData.h.in | 8 +- tests/src/cram/bam2sam.t | 63 + tests/src/cram/pbindexdump_cpp.t | 39 + tests/src/cram/pbindexdump_json.t | 83 + tests/src/cram/pbmerge_aligned_ordering.t | 197 + tests/src/cram/pbmerge_dataset.t | 144 + tests/src/cram/pbmerge_fofn.t | 134 + tests/src/cram/pbmerge_mixed_ordering.t | 57 + tests/src/cram/pbmerge_pacbio_ordering.t | 227 + tests/src/python/test/test_Accuracy.py | 24 +- tests/src/python/test/test_BamFile.py | 1 - tests/src/python/test/test_BamHeader.py | 8 +- tests/src/python/test/test_PolymeraseStitching.py | 383 + tests/src/test_Accuracy.cpp | 24 +- tests/src/test_AlignmentPrinter.cpp | 102 +- tests/src/test_BamFile.cpp | 108 + tests/src/test_BamHeader.cpp | 216 +- tests/src/test_BamRecord.cpp | 4 + tests/src/test_BamRecordClipping.cpp | 24 + tests/src/test_BamWriter.cpp | 27 + .../src/test_BarcodeQuery.cpp | 19 +- tests/src/test_Compare.cpp | 739 ++ tests/src/test_DataSetCore.cpp | 74 +- tests/src/test_DataSetIO.cpp | 436 +- tests/src/test_DataSetQuery.cpp | 126 +- tests/src/test_DataSetXsd.cpp | 80 +- tests/src/test_EndToEnd.cpp | 160 +- tests/src/test_EntireFileQuery.cpp | 3 +- tests/src/test_FileUtils.cpp | 325 + tests/src/test_GenomicIntervalQuery.cpp | 348 +- tests/src/test_PacBioIndex.cpp | 514 +- tests/src/test_PbiFilter.cpp | 1300 ++++ tests/src/test_PbiFilterQuery.cpp | 245 + tests/src/test_PolymeraseStitching.cpp | 191 +- .../{test_GroupQuery.cpp => test_QNameQuery.cpp} | 81 +- ...test_BamFile.cpp => test_ReadAccuracyQuery.cpp} | 39 +- tests/src/test_ReadGroupInfo.cpp | 64 +- tests/src/test_SequenceUtils.cpp | 24 - .../{test_TimeUtils.cpp => test_StringUtils.cpp} | 29 +- ...est_BamFile.cpp => test_SubreadLengthQuery.cpp} | 48 +- tests/src/test_Tags.cpp | 246 +- tests/src/test_TimeUtils.cpp | 16 +- .../src/test_VirtualPolymeraseCompositeReader.cpp | 132 + tools/CMakeLists.txt | 18 +- tools/bam2sam/CMakeLists.txt | 32 + tools/bam2sam/src/Bam2Sam.cpp | 121 + .../pbbam/Strand.h => tools/bam2sam/src/Bam2Sam.h | 24 +- .../bam2sam/src/Bam2SamVersion.h.in | 19 +- .../bam2sam/src/Settings.h | 33 +- tools/{pbindex => bam2sam}/src/main.cpp | 87 +- .../common/BamFileMerger.h | 65 +- tools/common/BamFileMerger.inl | 262 + tools/{pbindex/src => common}/OptionParser.cpp | 0 tools/{pbindex/src => common}/OptionParser.h | 0 tools/pbindex/CMakeLists.txt | 27 +- tools/pbindex/src/PbIndex.cpp | 2 +- tools/pbindex/src/main.cpp | 2 +- tools/pbindexdump/CMakeLists.txt | 35 + tools/pbindexdump/src/CppFormatter.cpp | 177 + .../pbindexdump/src/CppFormatter.h | 25 +- .../pbindexdump/src/IFormatter.h | 36 +- tools/pbindexdump/src/JsonFormatter.cpp | 195 + .../pbindexdump/src/JsonFormatter.h | 48 +- .../src/PbIndexDump.cpp} | 49 +- .../pbindexdump/src/PbIndexDump.h | 24 +- .../pbindexdump/src/PbIndexDumpVersion.h.in | 22 +- .../pbindexdump/src/Settings.h | 35 +- tools/pbindexdump/src/json.hpp | 7295 ++++++++++++++++++++ tools/{pbindex => pbindexdump}/src/main.cpp | 86 +- tools/pbmerge/CMakeLists.txt | 36 + .../pbmerge/src/PbMergeVersion.h.in | 19 +- tools/pbmerge/src/main.cpp | 174 + 562 files changed, 38529 insertions(+), 9895 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbbam.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
