[med-svn] [pbbam] 02/12: Merge tag 'upstream/0.5.0'
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 5 03:24:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository pbbam.
commit 0ea2ca61f850661dd7379a065f2d16f9a90f204d
Merge: b32b993 ce58675
Author: Afif Elghraoui <afif at ghraoui.name>
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 | 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/{ZmwQuery.h => BarcodeQuery.h} | 55 +-
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 +
.../pbbam/{ZmwGroupQuery.h => PbiFilterQuery.h} | 55 +-
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 -
include/pbbam/{ZmwQuery.h => ReadAccuracyQuery.h} | 62 +-
include/pbbam/ReadGroupInfo.h | 571 +-
include/pbbam/SamTagCodec.h | 26 +-
include/pbbam/SequenceInfo.h | 174 +-
include/pbbam/Strand.h | 13 +-
.../{ZmwGroupQuery.h => SubreadLengthQuery.h} | 58 +-
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 +-
include/pbbam/{TagCollection.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 +
.../BamRecordBuilder.inl} | 93 +-
include/pbbam/internal/BamRecordImpl.inl | 216 +
include/pbbam/internal/BamRecordSort.h | 138 -
.../pbbam/internal/Cigar.inl | 57 +-
.../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/test_TimeUtils.cpp => src/BarcodeQuery.cpp | 41 +-
.../IBamFileIterator.h => src/ChemistryTable.cpp | 50 +-
.../pbbam/Orientation.h => src/ChemistryTable.h | 20 +-
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 +
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tests/data/dataset/hdfsubread_dataset.xml | 2 +-
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tests/data/polymerase/production.polymerase.bam | Bin 25072 -> 25082 bytes
tests/data/polymerase/production.scraps.bam | Bin 13530 -> 13535 bytes
tests/data/polymerase/production.scraps.bam.pbi | Bin 0 -> 279 bytes
tests/data/polymerase/production.subreads.bam | Bin 14655 -> 14659 bytes
tests/data/polymerase/production.subreads.bam.pbi | Bin 0 -> 186 bytes
tests/data/polymerase/production_hq.hqregion.bam | Bin 15796 -> 15803 bytes
.../data/polymerase/production_hq.hqregion.bam.pbi | Bin 0 -> 90 bytes
tests/data/polymerase/production_hq.scraps.bam | Bin 10061 -> 10070 bytes
tests/data/polymerase/production_hq.scraps.bam.pbi | Bin 0 -> 104 bytes
.../polymerase/whitelist/internal.polymerase.bam | Bin 0 -> 400494 bytes
.../whitelist/internal.polymerase.bam.pbi | Bin 0 -> 105 bytes
.../data/polymerase/whitelist/internal.scraps.bam | Bin 0 -> 203149 bytes
.../polymerase/whitelist/internal.scraps.bam.pbi | Bin 0 -> 420 bytes
.../polymerase/whitelist/internal.subreads.bam | Bin 0 -> 218703 bytes
.../polymerase/whitelist/internal.subreads.bam.pbi | Bin 0 -> 264 bytes
.../data/polymerase/whitelist/scrapless.scraps.bam | Bin 0 -> 436 bytes
.../polymerase/whitelist/scrapless.scraps.bam.pbi | Bin 0 -> 65 bytes
.../polymerase/whitelist/scrapless.subreads.bam | Bin 0 -> 33466 bytes
.../whitelist/scrapless.subreads.bam.pbi | Bin 0 -> 113 bytes
tests/data/relative/a/test.bam | Bin 0 -> 351 bytes
tests/data/relative/b/test1.bam | Bin 0 -> 351 bytes
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 +
tests/data/test_group_query/test1.bam | Bin 2165 -> 2168 bytes
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 +-
...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(-)
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