[med-svn] [pbseqlib] branch master updated (cc3fa8a -> 8d343c8)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Oct 24 01:24:11 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository pbseqlib.
from cc3fa8a pbseqlib (0~20151014+gitbe5d1bf-2) unstable; urgency=medium
new a9fc23c Imported Upstream version 0~20160519
new 44cabd4 Merge tag 'upstream/0_20160519'
new 08c1e2f Drop patch where similar change made upstream
new 6ac23c2 Bump Standards-Version to 3.9.8
new 01b0afd Don't put libpbseq in Metapackages section
new 906f924 Use encrypted protocols for VCS
new 0b39653 Update email address and copyright years
new 30a555d Fix "clean" target
new 3e3eac1 Use O3 optimization
new 619b7c7 Use dh-exec to handle library installation
new 4c1ed3f Install libraries to main ldpath
new 9eeecc7 Drop patches
new 50dad38 Remove unnecessary definition in d/rules
new f3fb1c8 Imported Upstream version 0~20160705
new 3616095 Merge tag 'upstream/0_20160705'
new 50ac2db Move header files to avoid breaking relative paths
new a5d6cf3 Remove obsolete lintian override
new 8d343c8 add d/README.source to explain relationship with reverse-dependencies
The 18 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 | 19 +-
.../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 | 64 ++-
alignment/format/BAMPrinter.hpp | 28 +-
alignment/format/BAMPrinterImpl.hpp | 79 +---
alignment/format/CompareSequencesPrinter.hpp | 2 +-
alignment/format/CompareSequencesPrinterImpl.hpp | 4 +-
alignment/format/IntervalPrinter.hpp | 4 +-
alignment/format/SAMHeaderPrinter.cpp | 32 +-
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/control | 10 +-
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/libpbdata-dev.install | 2 +
debian/libpbdata-dev.install.in | 1 -
debian/libpbdata.install | 2 +
debian/libpbdata.install.in | 1 -
debian/libpbihdf-dev.install | 2 +
debian/libpbihdf-dev.install.in | 1 -
debian/libpbihdf.install | 2 +
debian/libpbihdf.install.in | 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 | 29 +-
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 | 221 ++++++---
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 +-
358 files changed, 5321 insertions(+), 3480 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 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 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
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 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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