This is an automated email from the git hooks/post-receive script. 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbseqlib.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit