[med-svn] [pbbam] branch upstream updated (e2fa066 -> ce58675)
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 5 03:24:44 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository pbbam.
from e2fa066 Imported Upstream version 0~20150813+git4e9e417+dfsg
new ce58675 Imported Upstream version 0.5.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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 | 2 +
docs/examples/code/Compare_FullName.txt | 2 +
docs/examples/code/Compare_LocalContextFlag.txt | 2 +
docs/examples/code/Compare_MapQuality.txt | 2 +
docs/examples/code/Compare_MovieName.txt | 2 +
docs/examples/code/Compare_NumDeletedBases.txt | 2 +
docs/examples/code/Compare_NumInsertedBases.txt | 2 +
docs/examples/code/Compare_NumMatches.txt | 2 +
docs/examples/code/Compare_NumMismatches.txt | 2 +
docs/examples/code/Compare_QueryEnd.txt | 2 +
docs/examples/code/Compare_QueryStart.txt | 2 +
docs/examples/code/Compare_ReadAccuracy.txt | 2 +
docs/examples/code/Compare_ReadGroupId.txt | 2 +
docs/examples/code/Compare_ReadGroupNumericId.txt | 2 +
docs/examples/code/Compare_ReferenceEnd.txt | 2 +
docs/examples/code/Compare_ReferenceId.txt | 2 +
docs/examples/code/Compare_ReferenceName.txt | 2 +
docs/examples/code/Compare_ReferenceStart.txt | 2 +
docs/examples/code/Compare_TypeFromOperator.txt | 2 +
docs/examples/code/Compare_TypeToName.txt | 2 +
docs/examples/code/Compare_Zmw.txt | 2 +
docs/examples/code/EntireFileQuery.txt | 15 +
docs/examples/code/EntireFileQuery_BamFilename.txt | 4 +
docs/examples/code/EntireFileQuery_NonConst.txt | 4 +
docs/examples/code/GenomicIntervalQuery.txt | 16 +
docs/examples/code/GenomicIntervalQuery_Reuse.txt | 8 +
docs/examples/code/PbiAlignedEndFilter.txt | 4 +
docs/examples/code/PbiAlignedLengthFilter.txt | 4 +
docs/examples/code/PbiAlignedStartFilter.txt | 4 +
docs/examples/code/PbiAlignedStrandFilter.txt | 5 +
docs/examples/code/PbiBarcodeFilter.txt | 17 +
docs/examples/code/PbiBarcodeForwardFilter.txt | 15 +
docs/examples/code/PbiBarcodeQualityFilter.txt | 5 +
docs/examples/code/PbiBarcodeReverseFilter.txt | 15 +
docs/examples/code/PbiBarcodesFilter.txt | 6 +
docs/examples/code/PbiBuilder_WithReader.txt | 30 +
docs/examples/code/PbiBuilder_WithWriter.txt | 12 +
docs/examples/code/PbiFilterQuery.txt | 22 +
docs/examples/code/PbiFilter_Composition.txt | 8 +
docs/examples/code/PbiFilter_CustomFilter.txt | 21 +
docs/examples/code/PbiFilter_Interface.txt | 1 +
docs/examples/code/PbiFilter_Intersection_Copy.txt | 3 +
docs/examples/code/PbiFilter_Intersection_Move.txt | 3 +
docs/examples/code/PbiFilter_Union_Copy.txt | 3 +
docs/examples/code/PbiFilter_Union_Move.txt | 3 +
docs/examples/code/PbiIdentityFilter.txt | 6 +
docs/examples/code/PbiLocalContextFilter.txt | 22 +
docs/examples/code/PbiMapQualityFilter.txt | 5 +
docs/examples/code/PbiMovieNameFilter.txt | 14 +
docs/examples/code/PbiNumDeletedBasesFilter.txt | 6 +
docs/examples/code/PbiNumInsertedBasesFilter.txt | 6 +
docs/examples/code/PbiNumMatchesFilter.txt | 6 +
docs/examples/code/PbiNumMismatchesFilter.txt | 6 +
docs/examples/code/PbiQueryEndFilter.txt | 5 +
docs/examples/code/PbiQueryLengthFilter.txt | 5 +
docs/examples/code/PbiQueryNameFilter.txt | 15 +
docs/examples/code/PbiQueryStartFilter.txt | 5 +
docs/examples/code/PbiReadAccuracyFilter.txt | 5 +
docs/examples/code/PbiReadGroupFilter.txt | 64 +
docs/examples/code/PbiReferenceEndFilter.txt | 5 +
docs/examples/code/PbiReferenceIdFilter.txt | 16 +
docs/examples/code/PbiReferenceNameFilter.txt | 15 +
docs/examples/code/PbiReferenceStartFilter.txt | 5 +
docs/examples/code/PbiZmwFilter.txt | 16 +
docs/examples/code/ReadAccuracyQuery.txt | 15 +
docs/examples/code/SubreadLengthQuery.txt | 15 +
docs/examples/code/Tag_AsciiCtor.txt | 10 +
docs/examples/code/ZmwGroupQuery.txt | 23 +
docs/examples/code/ZmwQuery.txt | 6 +
docs/examples/code/ZmwWhitelistVirtualReader.txt | 6 +
docs/examples/plaintext/AlignmentPrinterOutput.txt | 13 +
.../plaintext/PbiFilter_DataSetXmlFilters.txt | 14 +
docs/source/api/Accuracy.rst | 11 +
docs/source/api/AlignmentPrinter.rst | 11 +
docs/source/api/AlignmentSet.rst | 11 +
docs/source/api/BaiIndexedBamReader.rst | 11 +
docs/source/api/BamFile.rst | 11 +
docs/source/api/BamHeader.rst | 11 +
docs/source/api/BamReader.rst | 11 +
docs/source/api/BamRecord.rst | 17 +
docs/source/api/BamRecordBuilder.rst | 11 +
docs/source/api/BamRecordImpl.rst | 11 +
docs/source/api/BamRecordView.rst | 11 +
docs/source/api/BamTagCodec.rst | 11 +
docs/source/api/BamWriter.rst | 11 +
docs/source/api/BarcodeLookupData.rst | 11 +
docs/source/api/BarcodeQuery.rst | 11 +
docs/source/api/BarcodeSet.rst | 11 +
docs/source/api/BasicLookupData.rst | 11 +
docs/source/api/Cigar.rst | 11 +
docs/source/api/CigarOperation.rst | 13 +
docs/source/api/Compare.rst | 8 +
docs/source/api/Config.rst | 8 +
docs/source/api/ConsensusAlignmentSet.rst | 11 +
docs/source/api/ConsensusReadSet.rst | 11 +
docs/source/api/ContigSet.rst | 11 +
docs/source/api/DataSet.rst | 11 +
docs/source/api/DataSetBase.rst | 11 +
docs/source/api/DataSetMetadata.rst | 11 +
docs/source/api/EntireFileQuery.rst | 11 +
docs/source/api/ExtensionElement.rst | 11 +
docs/source/api/Extensions.rst | 11 +
docs/source/api/ExternalResource.rst | 11 +
docs/source/api/ExternalResources.rst | 11 +
docs/source/api/FileIndex.rst | 11 +
docs/source/api/FileIndices.rst | 11 +
docs/source/api/Filter.rst | 11 +
docs/source/api/Filters.rst | 11 +
docs/source/api/Frames.rst | 11 +
docs/source/api/GenomicInterval.rst | 11 +
.../api/GenomicIntervalCompositeBamReader.rst | 11 +
docs/source/api/GenomicIntervalQuery.rst | 11 +
docs/source/api/HdfSubreadSet.rst | 11 +
docs/source/api/IndexResultBlock.rst | 17 +
docs/source/api/IndexedFastaReader.rst | 11 +
docs/source/api/Interval.rst | 11 +
.../api/InvalidSequencingChemistryException.rst | 11 +
docs/source/api/LocalContextFlags.rst | 8 +
docs/source/api/MappedLookupData.rst | 11 +
docs/source/api/NamespaceInfo.rst | 11 +
docs/source/api/NamespaceRegistry.rst | 11 +
docs/source/api/OrderedLookup.rst | 11 +
docs/source/api/Orientation.rst | 8 +
docs/source/api/ParentTool.rst | 11 +
docs/source/api/PbiBuilder.rst | 11 +
docs/source/api/PbiFile.rst | 14 +
docs/source/api/PbiFilter.rst | 11 +
docs/source/api/PbiFilterCompositeBamReader.rst | 11 +
docs/source/api/PbiFilterQuery.rst | 11 +
docs/source/api/PbiFilterTypes.rst | 8 +
docs/source/api/PbiIndex.rst | 11 +
docs/source/api/PbiIndexedBamReader.rst | 11 +
docs/source/api/PbiRawBarcodeData.rst | 11 +
docs/source/api/PbiRawBasicData.rst | 11 +
docs/source/api/PbiRawData.rst | 11 +
docs/source/api/PbiRawMappedData.rst | 11 +
docs/source/api/PbiRawReferenceData.rst | 11 +
docs/source/api/PbiReferenceEntry.rst | 11 +
docs/source/api/Position.rst | 10 +
docs/source/api/ProgramInfo.rst | 11 +
docs/source/api/QNameQuery.rst | 11 +
docs/source/api/QualityValue.rst | 11 +
docs/source/api/QualityValues.rst | 11 +
docs/source/api/ReadAccuracyQuery.rst | 11 +
docs/source/api/ReadGroupInfo.rst | 21 +
docs/source/api/ReferenceLookupData.rst | 11 +
docs/source/api/ReferenceSet.rst | 11 +
docs/source/api/SamTagCodec.rst | 11 +
docs/source/api/SequenceInfo.rst | 11 +
docs/source/api/SequentialCompositeBamReader.rst | 11 +
docs/source/api/Strand.rst | 8 +
docs/source/api/SubDataSets.rst | 11 +
docs/source/api/SubreadLengthQuery.rst | 11 +
docs/source/api/SubreadSet.rst | 11 +
docs/source/api/Tag.rst | 15 +
docs/source/api/TagCollection.rst | 11 +
docs/source/api/UnorderedLookup.rst | 11 +
docs/source/api/VirtualPolymeraseBamRecord.rst | 11 +
.../api/VirtualPolymeraseCompositeReader.rst | 11 +
docs/source/api/VirtualPolymeraseReader.rst | 11 +
docs/source/api/VirtualRegion.rst | 11 +
docs/source/api/VirtualRegionType.rst | 8 +
docs/source/api/VirtualRegionTypeMap.rst | 11 +
docs/source/api/ZmwGroupQuery.rst | 11 +
docs/source/api/ZmwQuery.rst | 11 +
docs/source/api/ZmwWhitelistVirtualReader.rst | 11 +
docs/source/api_reference.rst | 12 +
docs/source/commandline_utilities.rst | 15 +
docs/source/conf.py | 332 +
docs/source/getting_started.rst | 144 +
docs/source/index.rst | 33 +
docs/source/pacbio-theme/static/headerGradient.jpg | Bin 0 -> 7099 bytes
docs/source/pacbio-theme/static/pacbio.css | 238 +
docs/source/pacbio-theme/static/pacbioLogo.png | Bin 0 -> 3128 bytes
docs/source/pacbio-theme/static/pygments.css | 55 +
docs/source/pacbio-theme/theme.conf | 4 +
docs/source/requirements.txt | 1 +
docs/source/swig_bindings.rst | 257 +
docs/source/tools/bam2sam.rst | 21 +
docs/source/tools/pbindex.rst | 18 +
docs/source/tools/pbindexdump.rst | 233 +
docs/source/tools/pbmerge.rst | 30 +
docs/specs/pbbam.rst | 631 ++
include/pbbam/Accuracy.h | 51 +-
include/pbbam/AlignmentPrinter.h | 55 +-
include/pbbam/BaiIndexedBamReader.h | 130 +
include/pbbam/BamFile.h | 105 +-
include/pbbam/BamHeader.h | 240 +-
include/pbbam/BamReader.h | 157 +-
include/pbbam/BamRecord.h | 1312 ++--
include/pbbam/BamRecordBuilder.h | 198 +-
include/pbbam/BamRecordImpl.h | 468 +-
include/pbbam/BamTagCodec.h | 73 +-
include/pbbam/BamWriter.h | 95 +-
include/pbbam/{ZmwGroupQuery.h => BarcodeQuery.h} | 56 +-
include/pbbam/Cigar.h | 66 +-
include/pbbam/CigarOperation.h | 90 +-
include/pbbam/Compare.h | 430 ++
include/pbbam/CompositeBamReader.h | 269 +
include/pbbam/Config.h | 111 +-
include/pbbam/DataSet.h | 620 +-
include/pbbam/DataSetTypes.h | 601 +-
include/pbbam/DataSetXsd.h | 54 +-
include/pbbam/EntireFileQuery.h | 49 +-
include/pbbam/Frames.h | 86 +-
include/pbbam/GenomicInterval.h | 144 +-
include/pbbam/GenomicIntervalQuery.h | 62 +-
include/pbbam/GroupQuery.h | 88 -
include/pbbam/GroupQueryBase.h | 214 -
include/pbbam/IndexedFastaReader.h | 120 +-
include/pbbam/Interval.h | 149 +-
include/pbbam/LocalContextFlags.h | 25 +-
include/pbbam/Orientation.h | 20 +-
include/pbbam/PbiBasicTypes.h | 108 +
include/pbbam/PbiBuilder.h | 143 +-
include/pbbam/PbiFile.h | 36 +-
include/pbbam/PbiFilter.h | 343 +
include/pbbam/{ZmwQuery.h => PbiFilterQuery.h} | 54 +-
include/pbbam/PbiFilterTypes.h | 1028 +++
include/pbbam/PbiIndex.h | 277 +-
include/pbbam/PbiIndexedBamReader.h | 174 +
include/pbbam/PbiLookupData.h | 718 ++
include/pbbam/PbiRawData.h | 398 +-
include/pbbam/Position.h | 13 +-
include/pbbam/ProgramInfo.h | 166 +-
include/pbbam/{BamReader.h => QNameQuery.h} | 96 +-
include/pbbam/QualityValue.h | 63 +-
include/pbbam/QualityValues.h | 203 +-
include/pbbam/QueryBase.h | 241 -
.../pbbam/{ZmwGroupQuery.h => ReadAccuracyQuery.h} | 63 +-
include/pbbam/ReadGroupInfo.h | 571 +-
include/pbbam/SamTagCodec.h | 26 +-
include/pbbam/SequenceInfo.h | 174 +-
include/pbbam/Strand.h | 13 +-
include/pbbam/{ZmwQuery.h => SubreadLengthQuery.h} | 57 +-
include/pbbam/Tag.h | 175 +-
include/pbbam/TagCollection.h | 12 +-
include/pbbam/ZmwGroupQuery.h | 43 +-
include/pbbam/ZmwQuery.h | 42 +-
.../{virtual/VirtualRegionType.h => ZmwType.h} | 29 +-
.../VirtualRegionTypeMap.h => ZmwTypeMap.h} | 25 +-
.../InvalidSequencingChemistryException.h} | 96 +-
.../pbbam/{Position.h => internal/Accuracy.inl} | 35 +-
include/pbbam/internal/BamHeader.inl | 154 +
include/pbbam/internal/BamRecord.inl | 166 +
.../{Accuracy.h => internal/BamRecordBuilder.inl} | 76 +-
include/pbbam/internal/BamRecordImpl.inl | 216 +
include/pbbam/internal/BamRecordSort.h | 138 -
.../pbbam/internal/Cigar.inl | 55 +-
.../CigarOperation.inl} | 127 +-
.../{SequentialMergeStrategy.h => Compare.inl} | 55 +-
include/pbbam/internal/CompositeBamReader.inl | 397 ++
include/pbbam/internal/DataSet.inl | 6 +-
include/pbbam/internal/DataSetBaseTypes.h | 11 +-
include/pbbam/internal/DataSetElement.h | 8 +-
include/pbbam/internal/DataSetElement.inl | 40 +-
include/pbbam/internal/DataSetTypes.inl | 6 +-
include/pbbam/{Accuracy.h => internal/Frames.inl} | 85 +-
.../GenomicInterval.inl} | 67 +-
include/pbbam/internal/IMergeStrategy.h | 67 -
.../pbbam/{Interval.h => internal/Interval.inl} | 116 +-
include/pbbam/internal/MergeStrategy.h | 239 -
.../pbbam/internal/PbiBasicTypes.inl | 56 +-
include/pbbam/internal/PbiFilter.inl | 312 +
include/pbbam/internal/PbiFilterTypes.inl | 553 ++
include/pbbam/internal/PbiIndex.inl | 165 +
include/pbbam/internal/PbiIndex_p.h | 931 ---
include/pbbam/internal/PbiIndex_p.inl | 927 ---
include/pbbam/internal/PbiLookupData.inl | 531 ++
include/pbbam/internal/PbiRawData.inl | 113 +
.../{ProgramInfo.h => internal/ProgramInfo.inl} | 105 +-
.../internal/{MergeItem.h => QualityValue.inl} | 52 +-
.../QualityValues.inl} | 99 +-
include/pbbam/internal/QueryBase.h | 152 +-
include/pbbam/internal/QueryBase.inl | 177 +
.../ReadGroupInfo.inl} | 286 +-
.../{SequenceInfo.h => internal/SequenceInfo.inl} | 111 +-
include/pbbam/internal/Tag.inl | 19 +-
include/pbbam/virtual/VirtualPolymeraseBamRecord.h | 109 +-
.../virtual/VirtualPolymeraseCompositeReader.h | 111 +
include/pbbam/virtual/VirtualPolymeraseReader.h | 96 +-
include/pbbam/virtual/VirtualRegion.h | 89 +-
include/pbbam/virtual/VirtualRegionType.h | 23 +-
include/pbbam/virtual/VirtualRegionTypeMap.h | 11 +-
include/pbbam/virtual/ZmwWhitelistVirtualReader.h | 151 +
src/Accuracy.cpp | 10 +-
src/AlignmentPrinter.cpp | 15 +-
src/BaiIndexedBamReader.cpp | 141 +
src/BamFile.cpp | 110 +-
src/BamHeader.cpp | 289 +-
src/BamReader.cpp | 189 +
src/BamRecord.cpp | 408 +-
src/BamRecordImpl.cpp | 240 +-
src/BamTagCodec.cpp | 76 +-
src/BamWriter.cpp | 80 +-
src/{FilterEngine.cpp => BarcodeQuery.cpp} | 54 +-
.../IBamFileIterator.h => src/ChemistryTable.cpp | 50 +-
src/{FofnReader.h => ChemistryTable.h} | 17 +-
src/Cigar.cpp | 8 +-
src/CigarOperation.cpp | 6 +-
src/Compare.cpp | 141 +
src/Config.cpp | 16 +-
src/DataSet.cpp | 143 +-
src/DataSetBaseTypes.cpp | 48 +-
src/DataSetElement.cpp | 4 +-
src/DataSetIO.cpp | 7 +-
src/DataSetTypes.cpp | 110 +-
src/DataSetUtils.h | 12 +
src/DataSetXsd.cpp | 177 +-
src/EntireFileQuery.cpp | 73 +-
src/FileUtils.cpp | 246 +
src/FileUtils.h | 145 +-
src/Frames.cpp | 10 +-
src/GenomicInterval.cpp | 7 +-
src/GenomicIntervalQuery.cpp | 113 +-
src/GroupQuery.cpp | 91 -
src/IndexedFastaReader.cpp | 37 +-
src/MemoryUtils.h | 9 +
src/PbiBuilder.cpp | 225 +-
src/PbiFile.cpp | 49 +-
src/PbiFilter.cpp | 249 +
src/{FilterEngine.cpp => PbiFilterQuery.cpp} | 56 +-
src/PbiFilterTypes.cpp | 313 +
src/PbiIndex.cpp | 143 +-
src/PbiIndexIO.cpp | 111 +-
src/PbiIndexIO.h | 8 +-
src/PbiIndexedBamReader.cpp | 187 +
src/PbiRawData.cpp | 215 +-
src/ProgramInfo.cpp | 6 +-
src/{FilterEngine.cpp => QNameQuery.cpp} | 88 +-
src/QualityValue.cpp | 6 +-
.../ReadAccuracyQuery.cpp | 44 +-
src/ReadGroupInfo.cpp | 503 +-
src/SamTagCodec.cpp | 26 +-
src/SequenceInfo.cpp | 6 +-
.../SubreadLengthQuery.cpp | 44 +-
src/Tag.cpp | 25 +-
src/TagCollection.cpp | 6 +-
src/TimeUtils.h | 19 +
src/VirtualPolymeraseBamRecord.cpp | 149 +-
src/VirtualPolymeraseCompositeReader.cpp | 146 +
src/VirtualPolymeraseReader.cpp | 286 +-
src/VirtualRegionTypeMap.cpp | 17 +-
src/XmlReader.cpp | 2 +-
src/XmlWriter.cpp | 83 +-
src/ZmwGroupQuery.cpp | 133 +-
src/ZmwQuery.cpp | 111 +-
src/{VirtualRegionTypeMap.cpp => ZmwTypeMap.cpp} | 20 +-
...aseReader.cpp => ZmwWhitelistVirtualReader.cpp} | 102 +-
src/files.cmake | 89 +-
src/swig/Accuracy.i | 4 +-
src/swig/BamFile.i | 13 +-
src/swig/BamHeader.i | 7 -
src/swig/BamRecord.i | 8 +-
src/swig/BamRecordBuilder.i | 6 +
src/swig/BamRecordImpl.i | 4 +-
src/swig/BamWriter.i | 5 +-
src/swig/CigarOperation.i | 2 -
src/swig/DataSet.i | 34 +-
src/swig/DataSetTypes.i | 59 +
src/swig/EntireFileQuery.i | 4 +-
src/swig/GenomicInterval.i | 4 +-
src/swig/GenomicIntervalQuery.i | 6 +-
src/swig/LocalContextFlags.i | 4 +
src/swig/PacBioBam.i | 43 +-
src/swig/PbiRawData.i | 12 +-
src/swig/Tag.i | 174 +-
src/swig/VirtualPolymeraseBamRecord.i | 24 +
src/swig/VirtualPolymeraseReader.i | 11 +
src/swig/VirtualRegion.i | 18 +
src/swig/ZmwWhitelistVirtualReader.i | 11 +
tests/CMakeLists.txt | 15 +-
tests/data/chunking/chunking.subreadset.xml | 65 +
.../chunking/chunking_emptyfilters.subreadset.xml | 59 +
.../chunking_missingfilters.subreadset.xml | 58 +
...20800000001823174110291514_s1_p0.1.subreads.bam | Bin 0 -> 1090276 bytes
...0000001823174110291514_s1_p0.1.subreads.bam.pbi | Bin 0 -> 4163 bytes
...20800000001823174110291514_s1_p0.2.subreads.bam | Bin 0 -> 980379 bytes
...0000001823174110291514_s1_p0.2.subreads.bam.pbi | Bin 0 -> 3933 bytes
...20800000001823174110291514_s1_p0.3.subreads.bam | Bin 0 -> 973029 bytes
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tests/data/dataset/ali1.xml | 2 +-
tests/data/dataset/ali2.xml | 2 +-
tests/data/dataset/ali3.xml | 2 +-
tests/data/dataset/ali4.xml | 2 +-
tests/data/dataset/bam_mapping.bam | Bin 169668 -> 169668 bytes
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tests/data/dataset/bam_mapping_1.bam | Bin 167530 -> 167530 bytes
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tests/data/dataset/bam_mapping_new.bam.pbi | Bin 0 -> 362 bytes
tests/data/dataset/bam_mapping_staggered.xml | 2 +-
tests/data/dataset/barcode.dataset.xml | 4 +-
tests/data/dataset/ccsread.dataset.xml | 2 +-
tests/data/dataset/contig.dataset.xml | 30 +-
tests/data/dataset/hdfsubread_dataset.xml | 2 +-
tests/data/dataset/lambda_contigs.xml | 6 +-
tests/data/dataset/malformed.xml | 84 +
tests/data/dataset/merge.fofn | 2 +
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tests/data/dataset/pbalchemy10kbp.xml | 2 +-
tests/data/dataset/reference.dataset.xml | 2 +-
tests/data/dataset/subread_dataset1.xml | 2 +-
tests/data/dataset/subread_dataset2.xml | 2 +-
tests/data/dataset/subread_dataset3.xml | 2 +-
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tests/data/ex2.bam | Bin 125999 -> 126008 bytes
tests/data/ex2.bam.bai | Bin 176 -> 176 bytes
tests/data/ex2.sam | 2 +-
tests/data/{ex2.bam => ex2_copy.bam} | Bin
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tests/data/phi29.bam | Bin 0 -> 71653 bytes
.../polymerase/consolidate.subread.dataset.xml | 38 +
.../filtered_resources.subread.dataset.xml | 67 +
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tests/data/polymerase/internal.polymerase.bam | Bin 134303 -> 133770 bytes
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tests/data/polymerase/internal.scraps.bam.pbi | Bin 0 -> 275 bytes
tests/data/polymerase/internal.subreads.bam | Bin 73590 -> 73170 bytes
tests/data/polymerase/internal.subreads.bam.pbi | Bin 0 -> 185 bytes
tests/data/polymerase/internal_hq.hqregion.bam | Bin 82035 -> 0 bytes
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tests/data/polymerase/internal_polymerase.fasta | 2 -
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tests/data/polymerase/production.subreads.bam | Bin 14655 -> 14659 bytes
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tests/data/relative/b/test2.bam | Bin 0 -> 351 bytes
tests/data/relative/relative.fofn | 3 +
tests/data/relative/relative.xml | 8 +
tests/data/relative/relative2.fofn | 4 +
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tests/data/test_group_query/test2.bam | Bin 13004 -> 13008 bytes
tests/data/test_group_query/test2.bam.pbi | Bin 194 -> 197 bytes
tests/data/test_group_query/test3.bam | Bin 19277 -> 19294 bytes
tests/data/truncated.bam | Bin 0 -> 200 bytes
tests/files.cmake | 12 +-
tests/scripts/cram.py | 516 ++
tests/src/R/test_pbbam.sh.in | 11 +-
tests/src/R/tests/test_Accuracy.R | 33 +-
tests/src/R/tests/test_BamFile.R | 3 +-
tests/src/R/tests/test_BamHeader.R | 8 +-
tests/src/R/tests/test_EndToEnd.R | 41 +-
tests/src/R/tests/test_Intervals.R | 52 +-
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 +-
...est_ZmwQuery.cpp => test_ReadAccuracyQuery.cpp} | 41 +-
tests/src/test_ReadGroupInfo.cpp | 64 +-
tests/src/test_SequenceUtils.cpp | 24 -
.../{test_TimeUtils.cpp => test_StringUtils.cpp} | 29 +-
...st_ZmwQuery.cpp => test_SubreadLengthQuery.cpp} | 50 +-
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 +
.../PbIndexVersion.h.in => bam2sam/src/Bam2Sam.h} | 20 +-
.../src/Bam2SamVersion.h.in} | 12 +-
.../src/PbIndex.h => bam2sam/src/Settings.h} | 31 +-
tools/{pbindex => bam2sam}/src/main.cpp | 87 +-
.../src/PbIndex.h => common/BamFileMerger.h} | 52 +-
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 +
.../src/CppFormatter.h} | 21 +-
.../src/IFormatter.h} | 31 +-
tools/pbindexdump/src/JsonFormatter.cpp | 195 +
.../pbindexdump/src/JsonFormatter.h | 48 +-
.../PbIndex.h => pbindexdump/src/PbIndexDump.cpp} | 51 +-
.../src/PbIndexDump.h} | 18 +-
.../src/PbIndexDumpVersion.h.in} | 12 +-
.../src/PbIndex.h => pbindexdump/src/Settings.h} | 33 +-
tools/pbindexdump/src/json.hpp | 7295 ++++++++++++++++++++
tools/{pbindex => pbindexdump}/src/main.cpp | 86 +-
tools/pbmerge/CMakeLists.txt | 36 +
.../src/PbMergeVersion.h.in} | 12 +-
tools/pbmerge/src/main.cpp | 174 +
562 files changed, 38510 insertions(+), 9851 deletions(-)
create mode 100644 .travis.yml
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create mode 100644 README.md
create mode 100644 cmake/FindCSharp.cmake
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create mode 100644 docs/source/api/ConsensusAlignmentSet.rst
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create mode 100644 docs/source/api/LocalContextFlags.rst
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create mode 100644 docs/source/api/PbiFilter.rst
create mode 100644 docs/source/api/PbiFilterCompositeBamReader.rst
create mode 100644 docs/source/api/PbiFilterQuery.rst
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create mode 100644 docs/source/api/PbiRawReferenceData.rst
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create mode 100644 docs/source/api/Position.rst
create mode 100644 docs/source/api/ProgramInfo.rst
create mode 100644 docs/source/api/QNameQuery.rst
create mode 100644 docs/source/api/QualityValue.rst
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create mode 100644 docs/source/api/ReadAccuracyQuery.rst
create mode 100644 docs/source/api/ReadGroupInfo.rst
create mode 100644 docs/source/api/ReferenceLookupData.rst
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create mode 100644 docs/source/api/SamTagCodec.rst
create mode 100644 docs/source/api/SequenceInfo.rst
create mode 100644 docs/source/api/SequentialCompositeBamReader.rst
create mode 100644 docs/source/api/Strand.rst
create mode 100644 docs/source/api/SubDataSets.rst
create mode 100644 docs/source/api/SubreadLengthQuery.rst
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create mode 100644 docs/source/api/Tag.rst
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create mode 100644 docs/source/api/VirtualPolymeraseBamRecord.rst
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create mode 100644 docs/source/api/VirtualRegion.rst
create mode 100644 docs/source/api/VirtualRegionType.rst
create mode 100644 docs/source/api/VirtualRegionTypeMap.rst
create mode 100644 docs/source/api/ZmwGroupQuery.rst
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create mode 100755 docs/source/conf.py
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create mode 100644 docs/source/pacbio-theme/static/pygments.css
create mode 100644 docs/source/pacbio-theme/theme.conf
create mode 100644 docs/source/requirements.txt
create mode 100644 docs/source/swig_bindings.rst
create mode 100644 docs/source/tools/bam2sam.rst
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create mode 100644 docs/source/tools/pbindexdump.rst
create mode 100644 docs/source/tools/pbmerge.rst
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delete mode 100644 include/pbbam/GroupQuery.h
delete mode 100644 include/pbbam/GroupQueryBase.h
create mode 100644 include/pbbam/PbiBasicTypes.h
create mode 100644 include/pbbam/PbiFilter.h
copy include/pbbam/{ZmwQuery.h => PbiFilterQuery.h} (58%)
create mode 100644 include/pbbam/PbiFilterTypes.h
create mode 100644 include/pbbam/PbiIndexedBamReader.h
create mode 100644 include/pbbam/PbiLookupData.h
copy include/pbbam/{BamReader.h => QNameQuery.h} (55%)
delete mode 100644 include/pbbam/QueryBase.h
copy include/pbbam/{ZmwGroupQuery.h => ReadAccuracyQuery.h} (54%)
copy include/pbbam/{ZmwQuery.h => SubreadLengthQuery.h} (55%)
copy include/pbbam/{virtual/VirtualRegionType.h => ZmwType.h} (84%)
copy include/pbbam/{virtual/VirtualRegionTypeMap.h => ZmwTypeMap.h} (83%)
copy include/pbbam/{BamReader.h => exception/InvalidSequencingChemistryException.h} (53%)
copy include/pbbam/{Position.h => internal/Accuracy.inl} (77%)
create mode 100644 include/pbbam/internal/BamHeader.inl
create mode 100644 include/pbbam/internal/BamRecord.inl
copy include/pbbam/{Accuracy.h => internal/BamRecordBuilder.inl} (55%)
create mode 100644 include/pbbam/internal/BamRecordImpl.inl
delete mode 100644 include/pbbam/internal/BamRecordSort.h
copy src/StringUtils.h => include/pbbam/internal/Cigar.inl (71%)
copy include/pbbam/{CigarOperation.h => internal/CigarOperation.inl} (51%)
rename include/pbbam/internal/{SequentialMergeStrategy.h => Compare.inl} (63%)
create mode 100644 include/pbbam/internal/CompositeBamReader.inl
copy include/pbbam/{Accuracy.h => internal/Frames.inl} (56%)
copy include/pbbam/{GenomicIntervalQuery.h => internal/GenomicInterval.inl} (55%)
delete mode 100644 include/pbbam/internal/IMergeStrategy.h
copy include/pbbam/{Interval.h => internal/Interval.inl} (57%)
delete mode 100644 include/pbbam/internal/MergeStrategy.h
copy src/FilterEngine.cpp => include/pbbam/internal/PbiBasicTypes.inl (71%)
create mode 100644 include/pbbam/internal/PbiFilter.inl
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copy include/pbbam/{SequenceInfo.h => internal/SequenceInfo.inl} (60%)
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copy src/{FilterEngine.cpp => BarcodeQuery.cpp} (72%)
rename include/pbbam/internal/IBamFileIterator.h => src/ChemistryTable.cpp (67%)
copy src/{FofnReader.h => ChemistryTable.h} (89%)
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rename src/{FilterEngine.cpp => QNameQuery.cpp} (53%)
copy tests/src/test_TimeUtils.cpp => src/ReadAccuracyQuery.cpp (65%)
copy tests/src/test_TimeUtils.cpp => src/SubreadLengthQuery.cpp (65%)
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create mode 100644 tests/data/chunking/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam
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create mode 100644 tests/data/chunking/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam
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create mode 100644 tests/data/polymerase/consolidate.subread.dataset.xml
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create mode 100644 tests/data/polymerase/production.scraps.bam.pbi
create mode 100644 tests/data/polymerase/production.subreads.bam.pbi
create mode 100644 tests/data/polymerase/production_hq.hqregion.bam.pbi
create mode 100644 tests/data/polymerase/production_hq.scraps.bam.pbi
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create mode 100644 tests/data/polymerase/whitelist/internal.subreads.bam
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create mode 100644 tests/data/polymerase/whitelist/scrapless.subreads.bam.pbi
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create mode 100755 tests/scripts/cram.py
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create mode 100644 tests/src/cram/pbindexdump_json.t
create mode 100644 tests/src/cram/pbmerge_aligned_ordering.t
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create mode 100644 tests/src/cram/pbmerge_pacbio_ordering.t
create mode 100755 tests/src/python/test/test_PolymeraseStitching.py
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create mode 100644 tests/src/test_Compare.cpp
create mode 100644 tests/src/test_FileUtils.cpp
create mode 100644 tests/src/test_PbiFilter.cpp
create mode 100644 tests/src/test_PbiFilterQuery.cpp
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copy tests/src/{test_ZmwQuery.cpp => test_ReadAccuracyQuery.cpp} (74%)
copy tests/src/{test_TimeUtils.cpp => test_StringUtils.cpp} (73%)
copy tests/src/{test_ZmwQuery.cpp => test_SubreadLengthQuery.cpp} (66%)
create mode 100644 tests/src/test_VirtualPolymeraseCompositeReader.cpp
create mode 100644 tools/bam2sam/CMakeLists.txt
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copy tools/{pbindex/src/PbIndex.h => bam2sam/src/Settings.h} (83%)
copy tools/{pbindex => bam2sam}/src/main.cpp (51%)
copy tools/{pbindex/src/PbIndex.h => common/BamFileMerger.h} (60%)
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copy tools/{pbindex/src/PbIndex.h => pbindexdump/src/PbIndexDump.cpp} (74%)
copy tools/{pbindex/src/PbIndexVersion.h.in => pbindexdump/src/PbIndexDump.h} (87%)
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copy tools/{pbindex/src/PbIndex.h => pbindexdump/src/Settings.h} (83%)
create mode 100644 tools/pbindexdump/src/json.hpp
copy tools/{pbindex => pbindexdump}/src/main.cpp (51%)
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copy tools/{pbindex/src/PbIndexVersion.h.in => pbmerge/src/PbMergeVersion.h.in} (90%)
create mode 100644 tools/pbmerge/src/main.cpp
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