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Import pbbam_0.7.4+ds.orig.tar.gz
authorAfif Elghraoui <afif@debian.org>
Sun, 22 Jan 2017 07:48:21 +0000 (07:48 +0000)
committerAfif Elghraoui <afif@debian.org>
Sun, 22 Jan 2017 07:48:21 +0000 (07:48 +0000)
commita4848319cda7670ead169ad844e7cfb3060c19be
tree2f8fcbce259b0ecc86ebf6ad0b62a0a81ae5dfc1tree | snapshot
Import pbbam_0.7.4+ds.orig.tar.gz

[dgit import orig pbbam_0.7.4+ds.orig.tar.gz]
704 files changed:
.gitignore [new file with mode: 0644] blob
.travis.yml [new file with mode: 0644] blob
CHANGELOG.md [new file with mode: 0644] blob
CMakeLists.txt [new file with mode: 0644] blob
INSTALL.md [new file with mode: 0644] blob
LICENSE.txt [new file with mode: 0644] blob
README.md [new file with mode: 0644] blob
cmake/FindCSharp.cmake [new file with mode: 0644] blob
cmake/FindDotNetFrameworkSdk.cmake [new file with mode: 0644] blob
cmake/FindMono.cmake [new file with mode: 0644] blob
cmake/FindR.cmake [new file with mode: 0644] blob
cmake/PbbamTool.cmake [new file with mode: 0644] blob
cmake/UseCSharp.cmake [new file with mode: 0644] blob
cmake/UseDotNetFrameworkSdk.cmake [new file with mode: 0644] blob
cmake/UseMono.cmake [new file with mode: 0644] blob
cmake/pbbam-ccache.cmake [new file with mode: 0644] blob
cmake/pbbam-compilerflags.cmake [new file with mode: 0644] blob
cmake/pbbam-dependencies.cmake [new file with mode: 0644] blob
cmake/pbbam-libtype.cmake [new file with mode: 0644] blob
docs/CMakeLists.txt [new file with mode: 0644] blob
docs/Doxyfile.in [new file with mode: 0644] blob
docs/Makefile [new file with mode: 0644] blob
docs/examples/code/BarcodeQuery.txt [new file with mode: 0644] blob
docs/examples/code/Compare.txt [new file with mode: 0644] blob
docs/examples/code/Compare_AlignedEnd.txt [new file with mode: 0644] blob
docs/examples/code/Compare_AlignedStart.txt [new file with mode: 0644] blob
docs/examples/code/Compare_AlignedStrand.txt [new file with mode: 0644] blob
docs/examples/code/Compare_BarcodeForward.txt [new file with mode: 0644] blob
docs/examples/code/Compare_BarcodeQuality.txt [new file with mode: 0644] blob
docs/examples/code/Compare_BarcodeReverse.txt [new file with mode: 0644] blob
docs/examples/code/Compare_FullName.txt [new file with mode: 0644] blob
docs/examples/code/Compare_LocalContextFlag.txt [new file with mode: 0644] blob
docs/examples/code/Compare_MapQuality.txt [new file with mode: 0644] blob
docs/examples/code/Compare_MovieName.txt [new file with mode: 0644] blob
docs/examples/code/Compare_NumDeletedBases.txt [new file with mode: 0644] blob
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docs/examples/code/Compare_NumMismatches.txt [new file with mode: 0644] blob
docs/examples/code/Compare_QueryEnd.txt [new file with mode: 0644] blob
docs/examples/code/Compare_QueryStart.txt [new file with mode: 0644] blob
docs/examples/code/Compare_ReadAccuracy.txt [new file with mode: 0644] blob
docs/examples/code/Compare_ReadGroupId.txt [new file with mode: 0644] blob
docs/examples/code/Compare_ReadGroupNumericId.txt [new file with mode: 0644] blob
docs/examples/code/Compare_ReferenceEnd.txt [new file with mode: 0644] blob
docs/examples/code/Compare_ReferenceId.txt [new file with mode: 0644] blob
docs/examples/code/Compare_ReferenceName.txt [new file with mode: 0644] blob
docs/examples/code/Compare_ReferenceStart.txt [new file with mode: 0644] blob
docs/examples/code/Compare_TypeFromOperator.txt [new file with mode: 0644] blob
docs/examples/code/Compare_TypeToName.txt [new file with mode: 0644] blob
docs/examples/code/Compare_Zmw.txt [new file with mode: 0644] blob
docs/examples/code/EntireFileQuery.txt [new file with mode: 0644] blob
docs/examples/code/EntireFileQuery_BamFilename.txt [new file with mode: 0644] blob
docs/examples/code/EntireFileQuery_NonConst.txt [new file with mode: 0644] blob
docs/examples/code/GenomicIntervalQuery.txt [new file with mode: 0644] blob
docs/examples/code/GenomicIntervalQuery_Reuse.txt [new file with mode: 0644] blob
docs/examples/code/PbiAlignedEndFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiAlignedLengthFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiAlignedStartFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiAlignedStrandFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiBarcodeFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiBarcodeForwardFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiBarcodeQualityFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiBarcodeReverseFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiBarcodesFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiBuilder_WithReader.txt [new file with mode: 0644] blob
docs/examples/code/PbiBuilder_WithWriter.txt [new file with mode: 0644] blob
docs/examples/code/PbiFilterQuery.txt [new file with mode: 0644] blob
docs/examples/code/PbiFilter_Composition.txt [new file with mode: 0644] blob
docs/examples/code/PbiFilter_CustomFilter.txt [new file with mode: 0644] blob
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docs/examples/code/PbiFilter_Intersection_Copy.txt [new file with mode: 0644] blob
docs/examples/code/PbiFilter_Intersection_Move.txt [new file with mode: 0644] blob
docs/examples/code/PbiFilter_Union_Copy.txt [new file with mode: 0644] blob
docs/examples/code/PbiFilter_Union_Move.txt [new file with mode: 0644] blob
docs/examples/code/PbiIdentityFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiLocalContextFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiMapQualityFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiMovieNameFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiNumDeletedBasesFilter.txt [new file with mode: 0644] blob
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docs/examples/code/PbiNumMatchesFilter.txt [new file with mode: 0644] blob
docs/examples/code/PbiNumMismatchesFilter.txt [new file with mode: 0644] blob
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docs/examples/code/PbiQueryNameFilter.txt [new file with mode: 0644] blob
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docs/examples/code/PbiReadAccuracyFilter.txt [new file with mode: 0644] blob
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docs/examples/code/PbiZmwFilter.txt [new file with mode: 0644] blob
docs/examples/code/ReadAccuracyQuery.txt [new file with mode: 0644] blob
docs/examples/code/SubreadLengthQuery.txt [new file with mode: 0644] blob
docs/examples/code/Tag_AsciiCtor.txt [new file with mode: 0644] blob
docs/examples/code/WhitelistedZmwReadStitcher.txt [new file with mode: 0644] blob
docs/examples/code/ZmwGroupQuery.txt [new file with mode: 0644] blob
docs/examples/code/ZmwQuery.txt [new file with mode: 0644] blob
docs/examples/plaintext/AlignmentPrinterOutput.txt [new file with mode: 0644] blob
docs/examples/plaintext/PbiFilter_DataSetXmlFilters.txt [new file with mode: 0644] blob
docs/source/api/Accuracy.rst [new file with mode: 0644] blob
docs/source/api/AlignmentPrinter.rst [new file with mode: 0644] blob
docs/source/api/AlignmentSet.rst [new file with mode: 0644] blob
docs/source/api/BaiIndexedBamReader.rst [new file with mode: 0644] blob
docs/source/api/BamFile.rst [new file with mode: 0644] blob
docs/source/api/BamHeader.rst [new file with mode: 0644] blob
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docs/source/api/BamRecord.rst [new file with mode: 0644] blob
docs/source/api/BamRecordBuilder.rst [new file with mode: 0644] blob
docs/source/api/BamRecordImpl.rst [new file with mode: 0644] blob
docs/source/api/BamRecordView.rst [new file with mode: 0644] blob
docs/source/api/BamTagCodec.rst [new file with mode: 0644] blob
docs/source/api/BamWriter.rst [new file with mode: 0644] blob
docs/source/api/BarcodeLookupData.rst [new file with mode: 0644] blob
docs/source/api/BarcodeQuery.rst [new file with mode: 0644] blob
docs/source/api/BarcodeSet.rst [new file with mode: 0644] blob
docs/source/api/BasicLookupData.rst [new file with mode: 0644] blob
docs/source/api/Cigar.rst [new file with mode: 0644] blob
docs/source/api/CigarOperation.rst [new file with mode: 0644] blob
docs/source/api/Compare.rst [new file with mode: 0644] blob
docs/source/api/Config.rst [new file with mode: 0644] blob
docs/source/api/ConsensusAlignmentSet.rst [new file with mode: 0644] blob
docs/source/api/ConsensusReadSet.rst [new file with mode: 0644] blob
docs/source/api/ContigSet.rst [new file with mode: 0644] blob
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docs/source/api/EntireFileQuery.rst [new file with mode: 0644] blob
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docs/source/api/Frames.rst [new file with mode: 0644] blob
docs/source/api/GenomicInterval.rst [new file with mode: 0644] blob
docs/source/api/GenomicIntervalCompositeBamReader.rst [new file with mode: 0644] blob
docs/source/api/GenomicIntervalQuery.rst [new file with mode: 0644] blob
docs/source/api/HdfSubreadSet.rst [new file with mode: 0644] blob
docs/source/api/IndexResultBlock.rst [new file with mode: 0644] blob
docs/source/api/IndexedFastaReader.rst [new file with mode: 0644] blob
docs/source/api/Interval.rst [new file with mode: 0644] blob
docs/source/api/InvalidSequencingChemistryException.rst [new file with mode: 0644] blob
docs/source/api/LocalContextFlags.rst [new file with mode: 0644] blob
docs/source/api/MappedLookupData.rst [new file with mode: 0644] blob
docs/source/api/NamespaceInfo.rst [new file with mode: 0644] blob
docs/source/api/NamespaceRegistry.rst [new file with mode: 0644] blob
docs/source/api/OrderedLookup.rst [new file with mode: 0644] blob
docs/source/api/Orientation.rst [new file with mode: 0644] blob
docs/source/api/ParentTool.rst [new file with mode: 0644] blob
docs/source/api/PbiBuilder.rst [new file with mode: 0644] blob
docs/source/api/PbiFile.rst [new file with mode: 0644] blob
docs/source/api/PbiFilter.rst [new file with mode: 0644] blob
docs/source/api/PbiFilterCompositeBamReader.rst [new file with mode: 0644] blob
docs/source/api/PbiFilterQuery.rst [new file with mode: 0644] blob
docs/source/api/PbiFilterTypes.rst [new file with mode: 0644] blob
docs/source/api/PbiIndex.rst [new file with mode: 0644] blob
docs/source/api/PbiIndexedBamReader.rst [new file with mode: 0644] blob
docs/source/api/PbiRawBarcodeData.rst [new file with mode: 0644] blob
docs/source/api/PbiRawBasicData.rst [new file with mode: 0644] blob
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docs/source/api/PbiRawReferenceData.rst [new file with mode: 0644] blob
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docs/source/api/Position.rst [new file with mode: 0644] blob
docs/source/api/ProgramInfo.rst [new file with mode: 0644] blob
docs/source/api/QNameQuery.rst [new file with mode: 0644] blob
docs/source/api/QualityValue.rst [new file with mode: 0644] blob
docs/source/api/QualityValues.rst [new file with mode: 0644] blob
docs/source/api/ReadAccuracyQuery.rst [new file with mode: 0644] blob
docs/source/api/ReadGroupInfo.rst [new file with mode: 0644] blob
docs/source/api/ReferenceLookupData.rst [new file with mode: 0644] blob
docs/source/api/ReferenceSet.rst [new file with mode: 0644] blob
docs/source/api/SamTagCodec.rst [new file with mode: 0644] blob
docs/source/api/SequenceInfo.rst [new file with mode: 0644] blob
docs/source/api/SequentialCompositeBamReader.rst [new file with mode: 0644] blob
docs/source/api/Strand.rst [new file with mode: 0644] blob
docs/source/api/SubDataSets.rst [new file with mode: 0644] blob
docs/source/api/SubreadLengthQuery.rst [new file with mode: 0644] blob
docs/source/api/SubreadSet.rst [new file with mode: 0644] blob
docs/source/api/Tag.rst [new file with mode: 0644] blob
docs/source/api/TagCollection.rst [new file with mode: 0644] blob
docs/source/api/UnorderedLookup.rst [new file with mode: 0644] blob
docs/source/api/VirtualPolymeraseBamRecord.rst [new file with mode: 0644] blob
docs/source/api/VirtualPolymeraseCompositeReader.rst [new file with mode: 0644] blob
docs/source/api/VirtualPolymeraseReader.rst [new file with mode: 0644] blob
docs/source/api/VirtualRegion.rst [new file with mode: 0644] blob
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docs/source/api/VirtualRegionTypeMap.rst [new file with mode: 0644] blob
docs/source/api/ZmwGroupQuery.rst [new file with mode: 0644] blob
docs/source/api/ZmwQuery.rst [new file with mode: 0644] blob
docs/source/api/ZmwWhitelistVirtualReader.rst [new file with mode: 0644] blob
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docs/specs/pbbam_updated_release3_2.rst [new file with mode: 0755] blob
include/pbbam/Accuracy.h [new file with mode: 0644] blob
include/pbbam/AlignmentPrinter.h [new file with mode: 0644] blob
include/pbbam/BaiIndexedBamReader.h [new file with mode: 0644] blob
include/pbbam/BamFile.h [new file with mode: 0644] blob
include/pbbam/BamHeader.h [new file with mode: 0644] blob
include/pbbam/BamReader.h [new file with mode: 0644] blob
include/pbbam/BamRecord.h [new file with mode: 0644] blob
include/pbbam/BamRecordBuilder.h [new file with mode: 0644] blob
include/pbbam/BamRecordImpl.h [new file with mode: 0644] blob
include/pbbam/BamRecordTag.h [new file with mode: 0644] blob
include/pbbam/BamRecordView.h [new file with mode: 0644] blob
include/pbbam/BamTagCodec.h [new file with mode: 0644] blob
include/pbbam/BamWriter.h [new file with mode: 0644] blob
include/pbbam/BarcodeQuery.h [new file with mode: 0644] blob
include/pbbam/Cigar.h [new file with mode: 0644] blob
include/pbbam/CigarOperation.h [new file with mode: 0644] blob
include/pbbam/ClipType.h [new file with mode: 0644] blob
include/pbbam/Compare.h [new file with mode: 0644] blob
include/pbbam/CompositeBamReader.h [new file with mode: 0644] blob
include/pbbam/Config.h [new file with mode: 0644] blob
include/pbbam/DataSet.h [new file with mode: 0644] blob
include/pbbam/DataSetTypes.h [new file with mode: 0644] blob
include/pbbam/DataSetXsd.h [new file with mode: 0644] blob
include/pbbam/EntireFileQuery.h [new file with mode: 0644] blob
include/pbbam/FastaReader.h [new file with mode: 0644] blob
include/pbbam/FastaSequence.h [new file with mode: 0644] blob
include/pbbam/FrameEncodingType.h [new file with mode: 0644] blob
include/pbbam/Frames.h [new file with mode: 0644] blob
include/pbbam/GenomicInterval.h [new file with mode: 0644] blob
include/pbbam/GenomicIntervalQuery.h [new file with mode: 0644] blob
include/pbbam/IRecordWriter.h [new file with mode: 0644] blob
include/pbbam/IndexedFastaReader.h [new file with mode: 0644] blob
include/pbbam/Interval.h [new file with mode: 0644] blob
include/pbbam/LocalContextFlags.h [new file with mode: 0644] blob
include/pbbam/MD5.h [new file with mode: 0644] blob
include/pbbam/Orientation.h [new file with mode: 0644] blob
include/pbbam/PbiBasicTypes.h [new file with mode: 0644] blob
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include/pbbam/PbiFile.h [new file with mode: 0644] blob
include/pbbam/PbiFilter.h [new file with mode: 0644] blob
include/pbbam/PbiFilterQuery.h [new file with mode: 0644] blob
include/pbbam/PbiFilterTypes.h [new file with mode: 0644] blob
include/pbbam/PbiIndex.h [new file with mode: 0644] blob
include/pbbam/PbiIndexedBamReader.h [new file with mode: 0644] blob
include/pbbam/PbiLookupData.h [new file with mode: 0644] blob
include/pbbam/PbiRawData.h [new file with mode: 0644] blob
include/pbbam/Position.h [new file with mode: 0644] blob
include/pbbam/ProgramInfo.h [new file with mode: 0644] blob
include/pbbam/PulseBehavior.h [new file with mode: 0644] blob
include/pbbam/QNameQuery.h [new file with mode: 0644] blob
include/pbbam/QualityValue.h [new file with mode: 0644] blob
include/pbbam/QualityValues.h [new file with mode: 0644] blob
include/pbbam/ReadAccuracyQuery.h [new file with mode: 0644] blob
include/pbbam/ReadGroupInfo.h [new file with mode: 0644] blob
include/pbbam/RecordType.h [new file with mode: 0644] blob
include/pbbam/SamTagCodec.h [new file with mode: 0644] blob
include/pbbam/SamWriter.h [new file with mode: 0644] blob
include/pbbam/SequenceInfo.h [new file with mode: 0644] blob
include/pbbam/Strand.h [new file with mode: 0644] blob
include/pbbam/SubreadLengthQuery.h [new file with mode: 0644] blob
include/pbbam/Tag.h [new file with mode: 0644] blob
include/pbbam/TagCollection.h [new file with mode: 0644] blob
include/pbbam/UnmappedReadsQuery.h [new file with mode: 0644] blob
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include/pbbam/ZmwGroupQuery.h [new file with mode: 0644] blob
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include/pbbam/ZmwType.h [new file with mode: 0644] blob
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include/pbbam/exception/InvalidSequencingChemistryException.h [new file with mode: 0644] blob
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include/pbbam/internal/BamHeader.inl [new file with mode: 0644] blob
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include/pbbam/internal/BamRecordView.inl [new file with mode: 0644] blob
include/pbbam/internal/Cigar.inl [new file with mode: 0644] blob
include/pbbam/internal/CigarOperation.inl [new file with mode: 0644] blob
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include/pbbam/internal/CompositeBamReader.inl [new file with mode: 0644] blob
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include/pbbam/internal/PbiBasicTypes.inl [new file with mode: 0644] blob
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include/pbbam/internal/QualityValue.inl [new file with mode: 0644] blob
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include/pbbam/internal/QueryBase.h [new file with mode: 0644] blob
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include/pbbam/internal/ReadGroupInfo.inl [new file with mode: 0644] blob
include/pbbam/internal/SequenceInfo.inl [new file with mode: 0644] blob
include/pbbam/internal/Tag.inl [new file with mode: 0644] blob
include/pbbam/internal/Validator.inl [new file with mode: 0644] blob
include/pbbam/virtual/VirtualPolymeraseBamRecord.h [new file with mode: 0644] blob
include/pbbam/virtual/VirtualPolymeraseCompositeReader.h [new file with mode: 0644] blob
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tools/pbmerge/CMakeLists.txt [new file with mode: 0644] blob
tools/pbmerge/src/PbMergeVersion.h.in [new file with mode: 0644] blob
tools/pbmerge/src/main.cpp [new file with mode: 0644] blob
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