[med-svn] [pbbam] branch master updated (b32b993 -> fa63ad5)
Afif Elghraoui
afif at moszumanska.debian.org
Tue Jul 5 03:24:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository pbbam.
from b32b993 Remove empty debian/docs file
new ce58675 Imported Upstream version 0.5.0
new 0ea2ca6 Merge tag 'upstream/0.5.0'
new 9b646db Prepare new revision
new 2eca927 Declare additional copyrights to avoid repacking tarball
new 7e7dfa0 Update patches
new 445daeb Update email addresses and copyright years
new e58abf7 Update Standards-Version to 3.9.8
new f5c37e7 Use encrypted protocol for VCS URLs
new 5573bb0 Clean up d/control and d/rules
new 5558d71 Use dh-exec for library installation rather than sed-within-d/rules
new f9eebad Set up build-time tests for command-line tools
new fa63ad5 Add binary package for command-line tools
The 12 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 +
debian/changelog | 6 +
debian/control | 66 +-
debian/copyright | 39 +-
debian/libpbbam.install | 2 +
debian/libpbbam.install.in | 1 -
...uilding-gtest => dont-try-building-gtest.patch} | 15 +-
debian/patches/gcc5 | 515 --
debian/patches/remove-bam2sam.patch | 18 +
debian/patches/series | 7 +-
debian/patches/set-samtools-path | 15 -
debian/patches/{ssl-md5 => ssl-md5.patch} | 6 +-
debian/pbbamtools.install | 1 +
debian/rules | 23 +-
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 -
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 +-
include/pbbam/{Strand.h => ZmwType.h} | 24 +-
.../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 +
.../BamRecordBuilder.inl} | 93 +-
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 +
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tests/data/dataset/barcode.dataset.xml | 4 +-
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tests/data/dataset/contig.dataset.xml | 30 +-
tests/data/dataset/hdfsubread_dataset.xml | 2 +-
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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 +
575 files changed, 38651 insertions(+), 10436 deletions(-)
create mode 100644 .travis.yml
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create mode 100644 cmake/FindCSharp.cmake
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create mode 100644 cmake/PbbamTool.cmake
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create mode 100644 include/pbbam/PbiFilterTypes.h
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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/{ZmwQuery.h => ReadAccuracyQuery.h} (54%)
copy include/pbbam/{ZmwGroupQuery.h => SubreadLengthQuery.h} (55%)
copy include/pbbam/{Strand.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%)
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copy include/pbbam/{DataSetXsd.h => internal/BamRecordBuilder.inl} (55%)
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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
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delete mode 100644 include/pbbam/internal/IMergeStrategy.h
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copy tests/src/test_TimeUtils.cpp => src/SubreadLengthQuery.cpp (65%)
create mode 100644 src/VirtualPolymeraseCompositeReader.cpp
copy src/{VirtualRegionTypeMap.cpp => ZmwTypeMap.cpp} (86%)
copy src/{VirtualPolymeraseReader.cpp => ZmwWhitelistVirtualReader.cpp} (50%)
create mode 100644 src/swig/VirtualPolymeraseBamRecord.i
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create mode 100644 tests/data/chunking/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam
create mode 100644 tests/data/chunking/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.2.subreads.bam.pbi
create mode 100644 tests/data/chunking/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam
create mode 100644 tests/data/chunking/m150404_101626_42267_c100807920800000001823174110291514_s1_p0.3.subreads.bam.pbi
create mode 100644 tests/data/dataset/bam_mapping_new.bam
create mode 100644 tests/data/dataset/bam_mapping_new.bam.pbi
create mode 100644 tests/data/dataset/malformed.xml
create mode 100644 tests/data/dataset/merge.fofn
copy tests/data/{ex2.bam => ex2_copy.bam} (100%)
copy tests/data/{ex2.bam.bai => ex2_copy.bam.bai} (100%)
create mode 100644 tests/data/phi29.bam
create mode 100644 tests/data/polymerase/consolidate.subread.dataset.xml
create mode 100644 tests/data/polymerase/filtered_resources.subread.dataset.xml
create mode 100644 tests/data/polymerase/internal.hqregions.bam
create mode 100644 tests/data/polymerase/internal.lqregions.bam
create mode 100644 tests/data/polymerase/internal.scraps.bam.pbi
create mode 100644 tests/data/polymerase/internal.subreads.bam.pbi
delete mode 100644 tests/data/polymerase/internal_hq.hqregion.bam
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delete mode 100644 tests/data/polymerase/internal_polymerase.fasta
create mode 100644 tests/data/polymerase/multiple_resources.subread.dataset.xml
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
create mode 100644 tests/data/polymerase/whitelist/internal.polymerase.bam
create mode 100644 tests/data/polymerase/whitelist/internal.polymerase.bam.pbi
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create mode 100644 tests/data/polymerase/whitelist/internal.scraps.bam.pbi
create mode 100644 tests/data/polymerase/whitelist/internal.subreads.bam
create mode 100644 tests/data/polymerase/whitelist/internal.subreads.bam.pbi
create mode 100644 tests/data/polymerase/whitelist/scrapless.scraps.bam
create mode 100644 tests/data/polymerase/whitelist/scrapless.scraps.bam.pbi
create mode 100644 tests/data/polymerase/whitelist/scrapless.subreads.bam
create mode 100644 tests/data/polymerase/whitelist/scrapless.subreads.bam.pbi
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create mode 100644 tests/data/relative/relative2.fofn
create mode 100644 tests/data/truncated.bam
create mode 100755 tests/scripts/cram.py
create mode 100644 tests/src/R/tests/test_PolymeraseStitching.R
create mode 100644 tests/src/cram/bam2sam.t
create mode 100644 tests/src/cram/pbindexdump_cpp.t
create mode 100644 tests/src/cram/pbindexdump_json.t
create mode 100644 tests/src/cram/pbmerge_aligned_ordering.t
create mode 100644 tests/src/cram/pbmerge_dataset.t
create mode 100644 tests/src/cram/pbmerge_fofn.t
create mode 100644 tests/src/cram/pbmerge_mixed_ordering.t
create mode 100644 tests/src/cram/pbmerge_pacbio_ordering.t
create mode 100755 tests/src/python/test/test_PolymeraseStitching.py
rename src/QueryBase.cpp => tests/src/test_BarcodeQuery.cpp (89%)
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
rename tests/src/{test_GroupQuery.cpp => test_QNameQuery.cpp} (57%)
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
create mode 100644 tools/bam2sam/src/Bam2Sam.cpp
copy tools/{pbindex/src/PbIndexVersion.h.in => bam2sam/src/Bam2Sam.h} (86%)
copy tools/{pbindex/src/PbIndexVersion.h.in => bam2sam/src/Bam2SamVersion.h.in} (90%)
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%)
create mode 100644 tools/common/BamFileMerger.inl
rename tools/{pbindex/src => common}/OptionParser.cpp (100%)
rename tools/{pbindex/src => common}/OptionParser.h (100%)
create mode 100644 tools/pbindexdump/CMakeLists.txt
create mode 100644 tools/pbindexdump/src/CppFormatter.cpp
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copy tools/{pbindex/src/PbIndexVersion.h.in => pbindexdump/src/IFormatter.h} (80%)
create mode 100644 tools/pbindexdump/src/JsonFormatter.cpp
rename include/pbbam/internal/FilterEngine.h => tools/pbindexdump/src/JsonFormatter.h (72%)
copy tools/{pbindex/src/PbIndex.h => pbindexdump/src/PbIndexDump.cpp} (74%)
copy tools/{pbindex/src/PbIndexVersion.h.in => pbindexdump/src/PbIndexDump.h} (87%)
copy tools/{pbindex/src/PbIndexVersion.h.in => pbindexdump/src/PbIndexDumpVersion.h.in} (89%)
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%)
create mode 100644 tools/pbmerge/CMakeLists.txt
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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