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afif pushed a change to branch debian/jessie-backports
in repository pbseqlib.
from 3d45427 pbseqlib (0~20151014+gitbe5d1bf-2~bpo8+1)
jessie-backports; urgency=medium
adds a9fc23c Imported Upstream version 0~20160519
adds 44cabd4 Merge tag 'upstream/0_20160519'
adds 08c1e2f Drop patch where similar change made upstream
adds 6ac23c2 Bump Standards-Version to 3.9.8
adds 01b0afd Don't put libpbseq in Metapackages section
adds 906f924 Use encrypted protocols for VCS
adds 0b39653 Update email address and copyright years
adds 30a555d Fix "clean" target
adds 3e3eac1 Use O3 optimization
adds 619b7c7 Use dh-exec to handle library installation
adds 4c1ed3f Install libraries to main ldpath
adds 9eeecc7 Drop patches
adds 50dad38 Remove unnecessary definition in d/rules
adds f3fb1c8 Imported Upstream version 0~20160705
adds 3616095 Merge tag 'upstream/0_20160705'
adds 50ac2db Move header files to avoid breaking relative paths
adds a5d6cf3 Remove obsolete lintian override
adds 8d343c8 add d/README.source to explain relationship with
reverse-dependencies
adds 0bde776 Add lintian-override for build artifact
adds a5d46e9 Add ldconfig triggers for libraries
adds c025a1d releasing package pbseqlib version 0~20160705-1
adds 727332e Build with pbbam
adds 17f27f2 releasing package pbseqlib version 0~20160705-2
adds 849e1e0 Imported Upstream version 0~20161219
adds 8935d3a Merge tag 'upstream/0_20161219'
adds a82b7e4 Update to debhelper compat 10
adds 1e2c59b releasing package pbseqlib version 0~20161219-1
new e1b2f60 Merge tag 'debian/0_20161219-1' into
debian/jessie-backports
new 2ee4340 releasing package pbseqlib version 0~20161219-1~bpo8+1
The 2 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:
.gitignore | 2 +
LICENSE | 100 ++++
alignment/MappingMetrics.cpp | 9 +-
.../algorithms/alignment/AffineGuidedAlign.hpp | 21 +-
.../algorithms/alignment/AffineKBandAlign.hpp | 34 +-
alignment/algorithms/alignment/AlignmentUtils.hpp | 6 +-
.../algorithms/alignment/AlignmentUtilsImpl.hpp | 10 +-
.../alignment/DistanceMatrixScoreFunctionImpl.hpp | 33 +-
alignment/algorithms/alignment/ExtendAlign.cpp | 6 +-
alignment/algorithms/alignment/ExtendAlign.hpp | 32 +-
alignment/algorithms/alignment/FullQVAlign.hpp | 14 +-
alignment/algorithms/alignment/GraphPaper.hpp | 4 +-
alignment/algorithms/alignment/GraphPaperImpl.hpp | 13 +-
alignment/algorithms/alignment/GuidedAlign.cpp | 30 +-
alignment/algorithms/alignment/GuidedAlign.hpp | 47 +-
.../algorithms/alignment/IDSScoreFunction.cpp | 15 +-
.../algorithms/alignment/IDSScoreFunction.hpp | 23 +-
alignment/algorithms/alignment/KBandAlign.cpp | 2 +-
alignment/algorithms/alignment/KBandAlign.hpp | 34 +-
alignment/algorithms/alignment/OneGapAlignment.hpp | 15 +-
.../alignment/QualityValueScoreFunction.cpp | 26 ++
.../alignment/QualityValueScoreFunction.hpp | 8 +-
alignment/algorithms/alignment/SDPAlign.hpp | 9 +-
alignment/algorithms/alignment/SDPAlignImpl.hpp | 35 +-
alignment/algorithms/alignment/SWAlignImpl.hpp | 19 +-
alignment/algorithms/alignment/sdp/SDPSetImpl.hpp | 2 +-
.../alignment/sdp/SparseDynamicProgramming.hpp | 10 +-
.../alignment/sdp/SparseDynamicProgrammingImpl.hpp | 8 +-
alignment/algorithms/anchoring/BWTSearch.cpp | 2 +-
alignment/algorithms/anchoring/BWTSearch.hpp | 10 +-
alignment/algorithms/anchoring/BasicEndpoint.hpp | 6 +-
.../algorithms/anchoring/BasicEndpointImpl.hpp | 2 +-
.../algorithms/anchoring/ClusterProbability.cpp | 2 +-
alignment/algorithms/anchoring/Coordinate.cpp | 2 +-
alignment/algorithms/anchoring/Coordinate.hpp | 2 +-
alignment/algorithms/anchoring/FindMaxInterval.cpp | 2 +-
alignment/algorithms/anchoring/FindMaxInterval.hpp | 19 +-
.../algorithms/anchoring/FindMaxIntervalImpl.hpp | 39 +-
alignment/algorithms/anchoring/GlobalChain.hpp | 10 +-
alignment/algorithms/anchoring/GlobalChainImpl.hpp | 12 +-
alignment/algorithms/anchoring/LISPValue.hpp | 8 +-
alignment/algorithms/anchoring/LISPValueImpl.hpp | 12 +-
.../algorithms/anchoring/LISPValueWeightor.hpp | 6 +-
.../algorithms/anchoring/LISPValueWeightorImpl.hpp | 8 +-
.../algorithms/anchoring/LISQValueWeightor.hpp | 7 +-
alignment/algorithms/anchoring/LISSizeWeightor.hpp | 4 +-
.../anchoring/LongestIncreasingSubsequence.hpp | 2 +-
.../anchoring/LongestIncreasingSubsequenceImpl.hpp | 6 +-
.../algorithms/anchoring/MapBySuffixArray.hpp | 12 +-
.../algorithms/anchoring/MapBySuffixArrayImpl.hpp | 24 +-
.../algorithms/anchoring/PrioritySearchTree.hpp | 4 +-
alignment/algorithms/anchoring/ScoreAnchors.hpp | 10 +-
.../algorithms/anchoring/ScoreAnchorsImpl.hpp | 14 +-
alignment/algorithms/sorting/DifferenceCovers.cpp | 7 +-
alignment/algorithms/sorting/DifferenceCovers.hpp | 4 +-
alignment/algorithms/sorting/Karkkainen.hpp | 10 +-
.../algorithms/sorting/LightweightSuffixArray.cpp | 29 +-
.../algorithms/sorting/LightweightSuffixArray.hpp | 7 +-
alignment/algorithms/sorting/MultikeyQuicksort.cpp | 16 +-
alignment/algorithms/sorting/MultikeyQuicksort.hpp | 9 +-
alignment/algorithms/sorting/qsufsort.hpp | 2 +-
alignment/anchoring/AnchorParameters.hpp | 4 +-
alignment/bwt/BWT.hpp | 13 +-
alignment/bwt/Occ.hpp | 10 +-
alignment/bwt/PackedHash.hpp | 8 +-
alignment/bwt/Pos.hpp | 6 +-
alignment/datastructures/alignment/Alignment.cpp | 48 +-
alignment/datastructures/alignment/Alignment.hpp | 4 +-
.../alignment/AlignmentCandidate.hpp | 6 +-
.../datastructures/alignment/AlignmentContext.hpp | 3 +-
.../datastructures/alignment/AlignmentMap.cpp | 2 +-
alignment/datastructures/alignment/ByteAlignment.h | 38 +-
alignment/datastructures/alignment/CmpFile.hpp | 17 +-
.../alignment/CmpIndexedStringTable.h | 3 +-
.../datastructures/alignment/FilterCriteria.cpp | 9 +-
.../datastructures/alignment/FilterCriteria.hpp | 3 +-
.../alignment/SAMToAlignmentCandidateAdapter.cpp | 48 +-
.../alignment/SAMToAlignmentCandidateAdapter.hpp | 23 +-
.../alignmentset/AlignmentSetToCmpH5Adapter.hpp | 8 +-
.../AlignmentSetToCmpH5AdapterImpl.hpp | 14 +-
.../alignmentset/SAMQVConversion.cpp | 2 +-
.../alignmentset/SAMSupplementalQVList.cpp | 3 +-
.../alignmentset/SAMSupplementalQVList.hpp | 2 +-
.../datastructures/anchoring/AnchorParameters.hpp | 8 +-
alignment/datastructures/anchoring/ClusterList.cpp | 2 +-
alignment/datastructures/anchoring/ClusterList.hpp | 2 +-
alignment/datastructures/anchoring/MatchPos.hpp | 18 +-
.../datastructures/anchoring/WeightedInterval.cpp | 13 +-
.../datastructures/anchoring/WeightedInterval.hpp | 8 +-
alignment/files/BaseSequenceIO.cpp | 22 +-
alignment/files/BaseSequenceIO.hpp | 2 +-
alignment/files/CCSIterator.cpp | 2 +-
alignment/files/CCSIterator.hpp | 2 +-
alignment/files/FragmentCCSIterator.cpp | 25 +-
alignment/files/FragmentCCSIterator.hpp | 6 +-
alignment/files/ReaderAgglomerate.cpp | 421 +++++++++++------
alignment/files/ReaderAgglomerate.hpp | 63 ++-
alignment/format/BAMPrinter.hpp | 30 +-
alignment/format/BAMPrinterImpl.hpp | 81 +---
alignment/format/CompareSequencesPrinter.hpp | 2 +-
alignment/format/CompareSequencesPrinterImpl.hpp | 4 +-
alignment/format/IntervalPrinter.hpp | 4 +-
alignment/format/SAMHeaderPrinter.cpp | 52 ++-
alignment/format/SAMHeaderPrinter.hpp | 16 +-
alignment/format/SAMPrinter.cpp | 56 ++-
alignment/format/SAMPrinter.hpp | 57 ++-
alignment/format/SAMPrinterImpl.hpp | 16 +-
alignment/format/StickAlignmentPrinter.hpp | 4 +-
alignment/format/SummaryPrinter.hpp | 4 +-
alignment/format/XMLPrinter.hpp | 1 +
alignment/ipc/SharedMemoryAllocator.hpp | 4 +-
alignment/makefile | 13 +-
alignment/query/PbiFilterZmwGroupQuery.cpp | 77 ++++
alignment/query/PbiFilterZmwGroupQuery.h | 37 ++
alignment/query/SequentialZmwGroupQuery.cpp | 71 +++
alignment/query/SequentialZmwGroupQuery.h | 35 ++
alignment/qvs/QualityValueProfile.hpp | 8 +-
alignment/simulator/CDFMap.hpp | 2 +-
alignment/simulator/ContextOutputList.hpp | 4 +-
alignment/simulator/ContextSample.cpp | 5 +-
alignment/simulator/ContextSample.hpp | 10 +-
alignment/simulator/LengthHistogram.cpp | 6 +-
alignment/simulator/LengthHistogram.hpp | 6 +-
alignment/simulator/OutputSample.hpp | 2 +-
alignment/simulator/OutputSampleListSet.hpp | 2 +-
alignment/simulator/QualitySample.hpp | 6 +-
alignment/statistics/AnchorDistributionTable.hpp | 20 +-
alignment/statistics/LookupAnchorDistribution.cpp | 45 +-
alignment/statistics/LookupAnchorDistribution.hpp | 2 +-
alignment/statistics/StatUtils.cpp | 3 +
alignment/statistics/StatUtilsImpl.hpp | 2 +-
alignment/statistics/VarianceAccumulator.hpp | 2 +-
alignment/statistics/pdfs.cpp | 6 -
alignment/statistics/pdfs.hpp | 2 -
alignment/suffixarray/LCPTable.hpp | 2 +-
alignment/suffixarray/SharedSuffixArray.hpp | 8 +-
alignment/suffixarray/SuffixArray.hpp | 32 +-
alignment/suffixarray/SuffixArrayTypes.hpp | 6 +-
alignment/suffixarray/ssort.hpp | 34 +-
alignment/tuples/BaseTuple.cpp | 26 +-
alignment/tuples/BaseTuple.hpp | 20 +-
alignment/tuples/CompressedDNATuple.hpp | 5 +-
alignment/tuples/DNATuple.cpp | 41 +-
alignment/tuples/DNATuple.hpp | 52 ++-
alignment/tuples/DNATupleImpl.hpp | 8 +-
alignment/tuples/HashedTupleList.hpp | 6 +-
alignment/tuples/TupleCountTable.hpp | 6 +-
alignment/tuples/TupleCountTableImpl.hpp | 6 +-
alignment/tuples/TupleList.hpp | 4 +-
alignment/tuples/TupleMask.h | 2 +-
alignment/tuples/TupleMatching.hpp | 10 +-
alignment/tuples/TupleMatchingImpl.hpp | 10 +-
alignment/tuples/TupleMetrics.cpp | 9 +-
alignment/tuples/TupleMetrics.hpp | 6 +-
alignment/tuples/tuple.h | 2 +-
alignment/utils/FileOfFileNames.cpp | 6 +-
alignment/utils/FileOfFileNames.hpp | 2 +-
alignment/utils/FileUtils.cpp | 2 +-
alignment/utils/FileUtils.hpp | 4 +-
alignment/utils/RangeUtils.hpp | 4 +-
alignment/utils/RegionUtils.cpp | 13 +-
alignment/utils/RegionUtils.hpp | 10 +-
alignment/utils/RegionUtilsImpl.hpp | 2 +
configure.py | 27 +-
debian/README.source | 13 +
debian/changelog | 40 ++
debian/compat | 2 +-
debian/control | 19 +-
debian/copyright | 4 +-
debian/libblasr-dev.install | 2 +
debian/libblasr-dev.install.in | 1 -
debian/libblasr.install | 2 +
debian/libblasr.install.in | 1 -
debian/libblasr.lintian-overrides | 1 -
debian/libblasr.triggers | 1 +
debian/libpbdata-dev.install | 2 +
debian/libpbdata-dev.install.in | 1 -
debian/libpbdata.install | 2 +
debian/libpbdata.install.in | 1 -
debian/libpbdata.triggers | 1 +
debian/libpbihdf-dev.install | 2 +
debian/libpbihdf-dev.install.in | 1 -
debian/libpbihdf.install | 2 +
debian/libpbihdf.install.in | 1 -
debian/libpbihdf.triggers | 1 +
debian/patches/32bit-narrowing-conversion.patch | 22 -
debian/patches/exclude-pbbam.patch | 33 --
debian/patches/external-gtest.patch | 34 --
debian/patches/series | 3 -
debian/rules | 34 +-
debian/source/lintian-overrides | 3 +
exports | 300 ++++++++++++
hdf/BufferedHDF2DArray.cpp | 8 +-
hdf/BufferedHDF2DArray.hpp | 35 +-
hdf/BufferedHDF2DArrayImpl.hpp | 52 ++-
hdf/BufferedHDFArray.cpp | 2 +-
hdf/BufferedHDFArray.hpp | 46 +-
hdf/BufferedHDFArrayImpl.hpp | 38 +-
hdf/HDFAlnGroupGroup.hpp | 2 +-
hdf/HDFAlnInfoGroup.hpp | 4 +-
hdf/HDFAlnInfoGroup.o.tmp.rm.login14-biofx01.11097 | Bin 0 -> 211992 bytes
hdf/HDFArray.hpp | 8 +-
hdf/HDFAtom.cpp | 12 +
hdf/HDFAtom.hpp | 22 +-
hdf/HDFAttributable.cpp | 1 +
hdf/HDFAttributable.hpp | 3 +-
hdf/HDFBasReader.cpp | 46 --
hdf/HDFBasReader.hpp | 127 +++--
hdf/HDFBasWriter.hpp | 10 +-
hdf/HDFBaseCallsWriter.cpp | 266 ++++++-----
hdf/HDFBaseCallsWriter.hpp | 162 +++----
hdf/HDFBaxWriter.cpp | 123 ++---
hdf/HDFBaxWriter.hpp | 131 ++----
hdf/HDFCCSReader.hpp | 1 +
hdf/HDFCmpExperimentGroup.hpp | 2 +-
hdf/HDFCmpFile.hpp | 61 ++-
hdf/HDFCmpReader.hpp | 21 +-
hdf/HDFCmpRefAlignmentGroup.hpp | 3 +-
hdf/HDFCmpRootGroup.hpp | 2 +-
hdf/HDFData.cpp | 2 +
hdf/HDFData.hpp | 2 +-
hdf/HDFFile.hpp | 2 +-
hdf/HDFFileLogGroup.hpp | 3 +-
hdf/HDFGroup.hpp | 5 +-
hdf/HDFMovieInfoGroup.hpp | 2 +-
hdf/HDFPlsReader.hpp | 33 +-
hdf/HDFPlsWriter.hpp | 7 +-
hdf/HDFPulseCallsWriter.cpp | 511 +++++++++++++++++++++
hdf/HDFPulseCallsWriter.hpp | 213 +++++++++
hdf/HDFPulseDataFile.cpp | 25 +-
hdf/HDFPulseDataFile.hpp | 41 +-
hdf/HDFPulseH5Writer.cpp | 0
hdf/HDFPulseWriter.cpp | 110 +++++
hdf/HDFPulseWriter.hpp | 102 ++++
hdf/HDFRefGroupGroup.hpp | 2 +-
hdf/HDFRefInfoGroup.hpp | 4 +-
hdf/HDFRegionTableReader.hpp | 4 +-
hdf/HDFRegionTableWriter.hpp | 6 +-
hdf/HDFRegionsWriter.cpp | 49 +-
hdf/HDFRegionsWriter.hpp | 41 +-
hdf/HDFSMRTSequenceReader.hpp | 1 +
hdf/HDFScanDataReader.hpp | 5 +-
hdf/HDFScanDataWriter.cpp | 92 ++--
hdf/HDFScanDataWriter.hpp | 65 ++-
hdf/HDFUtils.hpp | 2 +-
hdf/HDFWriteBuffer.hpp | 4 +-
hdf/HDFWriterBase.cpp | 90 ++--
hdf/HDFWriterBase.hpp | 158 +++++--
hdf/HDFZMWMetricsWriter.cpp | 43 +-
hdf/HDFZMWMetricsWriter.hpp | 37 +-
hdf/HDFZMWReader.cpp | 6 +-
hdf/HDFZMWReader.hpp | 10 +-
hdf/HDFZMWWriter.cpp | 212 ++++++---
hdf/HDFZMWWriter.hpp | 145 +++---
hdf/makefile | 10 +-
makefile | 2 +
pbdata/CCSSequence.hpp | 4 +-
pbdata/CommandLineParser.cpp | 83 ++--
pbdata/CommandLineParser.hpp | 40 +-
pbdata/CompressedSequence.hpp | 2 +-
pbdata/CompressedSequenceImpl.hpp | 9 +-
pbdata/DNASequence.cpp | 3 +-
pbdata/DNASequence.hpp | 2 +-
pbdata/Enumerations.h | 41 +-
pbdata/FASTAReader.cpp | 52 ++-
pbdata/FASTAReader.hpp | 14 +-
pbdata/FASTQReader.cpp | 12 +-
pbdata/FASTQReader.hpp | 2 +-
pbdata/FASTQSequence.cpp | 5 +-
pbdata/GFFFile.cpp | 1 +
pbdata/PacBioDefs.h | 84 ++--
pbdata/PackedDNASequence.cpp | 4 +-
pbdata/SMRTSequence.cpp | 225 ++++++---
pbdata/SMRTSequence.hpp | 76 ++-
pbdata/StringUtils.cpp | 4 +-
pbdata/StringUtils.hpp | 2 +-
pbdata/Types.h | 16 +-
pbdata/alignment/CmpAlignment.cpp | 11 +-
pbdata/alignment/CmpAlignment.hpp | 14 +-
pbdata/alignment/CmpAlignmentImpl.hpp | 2 +-
pbdata/amos/AfgBasWriter.cpp | 6 +-
pbdata/amos/AfgBasWriter.hpp | 5 +-
pbdata/loadpulses/MetricField.hpp | 2 +-
pbdata/loadpulses/MovieAlnIndexLookupTable.cpp | 16 +-
pbdata/loadpulses/MovieAlnIndexLookupTable.hpp | 44 +-
pbdata/makefile | 15 +-
pbdata/matrix/FlatMatrix.hpp | 2 +
pbdata/matrix/FlatMatrixImpl.hpp | 4 +-
pbdata/matrix/Matrix.hpp | 2 +-
pbdata/matrix/MatrixImpl.hpp | 6 +-
pbdata/metagenome/FindRandomSequence.hpp | 4 +-
pbdata/metagenome/SequenceIndexDatabase.hpp | 8 +-
pbdata/metagenome/SequenceIndexDatabaseImpl.hpp | 8 +-
pbdata/metagenome/TitleTable.hpp | 2 +-
pbdata/qvs/QualityValue.cpp | 2 +-
pbdata/qvs/QualityValue.hpp | 2 +-
pbdata/qvs/QualityValueVector.hpp | 14 +-
pbdata/qvs/QualityValueVectorImpl.hpp | 21 +-
pbdata/reads/AcqParams.cpp | 11 +
pbdata/reads/AcqParams.hpp | 25 +
pbdata/reads/BaseFile.cpp | 6 +-
pbdata/reads/BaseFile.hpp | 19 +-
pbdata/reads/BaseFileImpl.hpp | 2 +-
pbdata/reads/HoleXY.hpp | 3 +
pbdata/reads/PulseBaseCommon.cpp | 35 --
pbdata/reads/PulseBaseCommon.hpp | 35 --
pbdata/reads/PulseFile.cpp | 73 +--
pbdata/reads/PulseFile.hpp | 46 +-
pbdata/reads/PulseFileImpl.hpp | 13 +-
pbdata/reads/ReadInterval.hpp | 8 +
pbdata/reads/RegionAnnotation.cpp | 35 --
pbdata/reads/RegionAnnotation.hpp | 44 +-
pbdata/reads/RegionAnnotations.cpp | 49 +-
pbdata/reads/RegionAnnotations.hpp | 35 --
pbdata/reads/RegionTable.cpp | 39 +-
pbdata/reads/RegionTable.hpp | 41 +-
pbdata/reads/RegionTypeMap.cpp | 35 --
pbdata/reads/RegionTypeMap.hpp | 39 +-
pbdata/reads/ScanData.cpp | 73 +--
pbdata/reads/ScanData.hpp | 47 +-
pbdata/reads/ZMWGroupEntry.cpp | 2 +-
pbdata/reads/ZMWGroupEntry.hpp | 4 +-
pbdata/saf/AlnGroup.cpp | 5 +-
pbdata/saf/AlnGroup.hpp | 2 +-
pbdata/saf/AlnInfo.hpp | 4 +-
pbdata/saf/MovieInfo.cpp | 5 +-
pbdata/saf/MovieInfo.hpp | 4 +-
pbdata/saf/RefGroup.cpp | 10 +-
pbdata/saf/RefGroup.hpp | 4 +-
pbdata/saf/RefInfo.cpp | 3 +-
pbdata/sam/AlignmentSet.hpp | 10 +-
pbdata/sam/AlignmentSetImpl.hpp | 2 +-
pbdata/sam/ReadGroup.cpp | 10 +-
pbdata/sam/ReadGroup.hpp | 6 +-
pbdata/sam/ReferenceSequence.cpp | 13 +-
pbdata/sam/ReferenceSequence.hpp | 10 +-
pbdata/sam/SAMAlignment.cpp | 9 +-
pbdata/sam/SAMAlignment.hpp | 6 +-
pbdata/sam/SAMHeader.cpp | 3 +-
pbdata/sam/SAMHeader.hpp | 2 +-
pbdata/sam/SAMKeywordValuePair.cpp | 5 +-
pbdata/sam/SAMKeywordValuePair.hpp | 2 +-
pbdata/sam/SAMReader.hpp | 16 +-
pbdata/sam/SAMReaderImpl.hpp | 3 +-
pbdata/utils.hpp | 2 +-
pbdata/utils/BitUtils.cpp | 7 -
pbdata/utils/BitUtils.hpp | 2 +-
pbdata/utils/SMRTReadUtils.cpp | 4 +-
pbdata/utils/SMRTReadUtils.hpp | 4 +-
pbdata/utils/SMRTTitle.cpp | 2 +-
pbdata/utils/SMRTTitle.hpp | 4 +-
{alignment => pbdata}/utils/TimeUtils.cpp | 2 +-
{alignment => pbdata}/utils/TimeUtils.hpp | 0
pbdata/utilsImpl.hpp | 2 +-
rules.mk | 1 +
travis.sh | 6 +-
.../alignment/files/ReaderAgglomerate_gtest.cpp | 88 +++-
unittest/alignment/format/SAMPrinter_gtest.cpp | 58 ++-
.../query/PbiFilterZmwGroupQuery_gtest.cpp | 87 ++++
.../query/SequentialZmwGroupQuery_gtest.cpp | 70 +++
unittest/makefile | 17 +-
unittest/pbdata/SMRTSequence_gtest.cpp | 206 ++++++++-
unittest/pbdata/qvs/QualityValueVector_gtest.cpp | 33 ++
unittest/pbdata/testdata.h | 12 +-
364 files changed, 5390 insertions(+), 3510 deletions(-)
create mode 100644 LICENSE
create mode 100644 alignment/query/PbiFilterZmwGroupQuery.cpp
create mode 100644 alignment/query/PbiFilterZmwGroupQuery.h
create mode 100644 alignment/query/SequentialZmwGroupQuery.cpp
create mode 100644 alignment/query/SequentialZmwGroupQuery.h
create mode 100644 debian/README.source
create mode 100755 debian/libblasr-dev.install
delete mode 100644 debian/libblasr-dev.install.in
create mode 100755 debian/libblasr.install
delete mode 100644 debian/libblasr.install.in
delete mode 100644 debian/libblasr.lintian-overrides
create mode 100644 debian/libblasr.triggers
create mode 100755 debian/libpbdata-dev.install
delete mode 100644 debian/libpbdata-dev.install.in
create mode 100755 debian/libpbdata.install
delete mode 100644 debian/libpbdata.install.in
create mode 100644 debian/libpbdata.triggers
create mode 100755 debian/libpbihdf-dev.install
delete mode 100644 debian/libpbihdf-dev.install.in
create mode 100755 debian/libpbihdf.install
delete mode 100644 debian/libpbihdf.install.in
create mode 100644 debian/libpbihdf.triggers
delete mode 100644 debian/patches/32bit-narrowing-conversion.patch
delete mode 100644 debian/patches/exclude-pbbam.patch
delete mode 100644 debian/patches/external-gtest.patch
delete mode 100644 debian/patches/series
create mode 100644 debian/source/lintian-overrides
create mode 100644 exports
create mode 100644 hdf/HDFAlnInfoGroup.o.tmp.rm.login14-biofx01.11097
delete mode 100644 hdf/HDFBasReader.cpp
create mode 100644 hdf/HDFPulseCallsWriter.cpp
create mode 100644 hdf/HDFPulseCallsWriter.hpp
create mode 100644 hdf/HDFPulseH5Writer.cpp
create mode 100644 hdf/HDFPulseWriter.cpp
create mode 100644 hdf/HDFPulseWriter.hpp
create mode 100644 pbdata/reads/AcqParams.cpp
create mode 100644 pbdata/reads/AcqParams.hpp
rename {alignment => pbdata}/utils/TimeUtils.cpp (95%)
rename {alignment => pbdata}/utils/TimeUtils.hpp (100%)
create mode 100644 unittest/alignment/query/PbiFilterZmwGroupQuery_gtest.cpp
create mode 100644 unittest/alignment/query/SequentialZmwGroupQuery_gtest.cpp
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