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commit 5fb94eed78fa008b1bfd91b9c3e89cec553ab582 Merge: 007467b a9374dc Author: Afif Elghraoui <[email protected]> Date: Sun Dec 18 21:18:05 2016 -0800 Merge tag 'upstream/0.7.4+ds' Upstream version 0.7.4+ds CHANGELOG.md | 39 +- CMakeLists.txt | 165 +-- cmake/PbbamTool.cmake | 6 +- cmake/pbbam-ccache.cmake | 8 + cmake/pbbam-compilerflags.cmake | 44 + cmake/pbbam-dependencies.cmake | 23 + cmake/pbbam-libtype.cmake | 21 + docs/source/conf.py | 4 +- docs/specs/pbbam_structure.png | Bin 0 -> 23521 bytes docs/specs/pbbam_updated_release3_2.rst | 618 ++++++++++ include/pbbam/Config.h | 37 + .../ValidationException.h => FastaReader.h} | 86 +- .../TestData.h.in => include/pbbam/FastaSequence.h | 70 +- .../InvalidSequencingChemistryException.h | 7 +- include/pbbam/exception/ValidationException.h | 6 +- .../pbbam/internal/FastaSequence.inl | 33 +- include/pbbam/internal/ReadGroupInfo.inl | 1 + src/BamHeader.cpp | 41 +- src/BamRecord.cpp | 2 +- src/CMakeLists.txt | 112 +- src/ChemistryTable.cpp | 13 +- src/DataSet.cpp | 42 +- src/FastaReader.cpp | 155 +++ src/PbiFilter.cpp | 85 +- src/PbiIndexedBamReader.cpp | 4 +- src/Pulse2BaseCache.h | 2 +- src/SequenceUtils.h | 2 +- src/files.cmake | 4 + src/swig/CMakeLists.txt | 2 +- src/swig/WrapCSharp.cmake | 2 +- src/swig/WrapPython.cmake | 3 +- tests/CMakeLists.txt | 136 ++- tests/data/dataset/malformed.xml | 3 +- tests/data/empty.bam | Bin 0 -> 350 bytes tests/data/empty.bam.pbi | Bin 0 -> 67 bytes tests/data/phi29.bam.pbi | Bin 0 -> 1394 bytes tests/files.cmake | 1 + tests/scripts/generate_data.py | 24 + tests/src/CSharp/buildAssembly.sh.in | 8 +- tests/src/TestData.h.in | 1 + tests/src/cram/{bam2sam.t => bam2sam.t.in} | 4 +- .../{pbindexdump_cpp.t => pbindexdump_cpp.t.in} | 4 +- .../{pbindexdump_json.t => pbindexdump_json.t.in} | 4 +- ...ed_ordering.t => pbmerge_aligned_ordering.t.in} | 16 +- .../{pbmerge_dataset.t => pbmerge_dataset.t.in} | 14 +- .../src/cram/{pbmerge_fofn.t => pbmerge_fofn.t.in} | 12 +- ...ixed_ordering.t => pbmerge_mixed_ordering.t.in} | 6 +- ...bio_ordering.t => pbmerge_pacbio_ordering.t.in} | 16 +- tests/src/test_BamHeader.cpp | 12 +- tests/src/test_BamRecord.cpp | 1231 ++++++++++++++++++++ tests/src/test_BamWriter.cpp | 2 +- tests/src/test_DataSetCore.cpp | 1 + tests/src/test_DataSetIO.cpp | 4 +- tests/src/test_DataSetQuery.cpp | 2 +- tests/src/test_EndToEnd.cpp | 4 +- tests/src/test_Fasta.cpp | 105 ++ tests/src/test_FileUtils.cpp | 7 +- tests/src/test_PacBioIndex.cpp | 10 +- tests/src/test_PbiFilterQuery.cpp | 187 ++- tests/src/test_ReadGroupInfo.cpp | 25 + tests/src/test_SamWriter.cpp | 4 +- tools/CMakeLists.txt | 58 +- tools/bam2sam/CMakeLists.txt | 11 +- tools/pbindex/CMakeLists.txt | 2 +- tools/pbindexdump/CMakeLists.txt | 18 +- tools/pbmerge/CMakeLists.txt | 52 +- 66 files changed, 3148 insertions(+), 473 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
