[med-svn] [blasr] branch master updated (5430650 -> 01a382e)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Dec 14 21:14:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch master
in repository blasr.
from 5430650 Upload to unstable
new f0cc9fd Don't install LICENSES.txt file
new df881fc Prepare for new revision
new 255f617 Imported Upstream version 0~20150925+git77862af
new 7181937 Merge tag 'upstream/0_20150925+git77862af'
new b282ecd Imported Upstream version 0~20151014+git8e668be
new 74cd687 Merge tag 'upstream/0_20151014+git8e668be'
new 18e9b0d Use externally packaged pbseqlib and dynamically link to it
new df2d171 Adjust for renamed upstream documentation
new 595448b Minor clean-ups
new a77429b Update comment about why tests can't be run
new 0298c38 Allow building in parallel
new 01a382e Fix library linking
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:
.gitignore | 4 +
Blasr.cpp | 4333 +-
MANUAL.md | 84 -
Makefile | 59 -
MappingSemaphores.h | 45 -
README.INSTALL.md | 86 +
README.MANUAL.md | 38 +
README.md | 52 +-
blasr_git_common.mk | 15 -
blasr_gitp4.mk | 24 -
common.mk | 139 -
configure.py | 125 +-
ctest/affineAlign.t | 2 +-
ctest/hitpolicy.t | 14 +-
ctest/useccsallLargeGenome.t | 3 +-
debian/changelog | 6 +
debian/control | 20 +-
debian/copyright | 61 -
debian/docs | 3 +-
debian/get-orig-source | 39 -
debian/patches/selective-static-linking | 31 -
debian/patches/series | 1 -
debian/rules | 29 +-
extrautils/GNUmakefile | 45 -
extrautils/Makefile | 78 -
extrautils/makefile | 49 +
extrautils/p4.mk | 79 -
include/BlasrAlign.hpp | 122 +
include/BlasrAlignImpl.hpp | 1564 +
include/BlasrHeaders.h | 149 +
include/BlasrMiscs.hpp | 100 +
include/BlasrMiscsImpl.hpp | 223 +
include/BlasrUtils.hpp | 199 +
include/BlasrUtilsImpl.hpp | 1225 +
include/MappingBuffers.hpp | 116 +
MappingIPC.h => include/MappingIPC.h | 4 +-
MappingParameters.h => include/MappingParameters.h | 40 +-
include/MappingSemaphores.h | 45 +
include/ReadAlignments.hpp | 199 +
.../RegisterBlasrOptions.h | 62 +-
.../RegisterFilterOptions.h | 30 +-
libcpp.makefile | 9 -
libcpp/.gitignore | 7 -
libcpp/.travis.yml | 22 -
libcpp/README.md | 47 -
libcpp/alignment/MappingMetrics.cpp | 299 -
libcpp/alignment/MappingMetrics.hpp | 133 -
.../algorithms/alignment/AffineGuidedAlign.hpp | 589 -
.../algorithms/alignment/AffineKBandAlign.hpp | 406 -
.../algorithms/alignment/AlignmentFormats.hpp | 6 -
.../algorithms/alignment/AlignmentUtils.cpp | 43 -
.../algorithms/alignment/AlignmentUtils.hpp | 139 -
.../algorithms/alignment/AlignmentUtilsImpl.hpp | 548 -
.../algorithms/alignment/BaseScoreFunction.cpp | 11 -
.../algorithms/alignment/BaseScoreFunction.hpp | 17 -
.../alignment/DistanceMatrixScoreFunction.hpp | 40 -
.../alignment/DistanceMatrixScoreFunctionImpl.hpp | 96 -
.../alignment/algorithms/alignment/ExtendAlign.cpp | 79 -
.../alignment/algorithms/alignment/ExtendAlign.hpp | 416 -
.../alignment/algorithms/alignment/FullQVAlign.hpp | 132 -
.../alignment/algorithms/alignment/GraphPaper.hpp | 31 -
.../algorithms/alignment/GraphPaperImpl.hpp | 175 -
.../alignment/algorithms/alignment/GuidedAlign.cpp | 226 -
.../alignment/algorithms/alignment/GuidedAlign.hpp | 600 -
.../algorithms/alignment/IDSScoreFunction.cpp | 158 -
.../algorithms/alignment/IDSScoreFunction.hpp | 109 -
.../alignment/algorithms/alignment/KBandAlign.cpp | 30 -
.../alignment/algorithms/alignment/KBandAlign.hpp | 381 -
.../algorithms/alignment/OneGapAlignment.hpp | 374 -
.../alignment/QualityValueScoreFunction.cpp | 90 -
.../alignment/QualityValueScoreFunction.hpp | 56 -
libcpp/alignment/algorithms/alignment/SDPAlign.hpp | 64 -
.../algorithms/alignment/SDPAlignImpl.hpp | 614 -
libcpp/alignment/algorithms/alignment/SWAlign.hpp | 17 -
.../alignment/algorithms/alignment/SWAlignImpl.hpp | 389 -
.../algorithms/alignment/ScoreMatrices.cpp | 58 -
.../algorithms/alignment/ScoreMatrices.hpp | 18 -
.../algorithms/alignment/StringToScoreMatrix.cpp | 26 -
.../algorithms/alignment/StringToScoreMatrix.hpp | 9 -
.../algorithms/alignment/sdp/FragmentSort.hpp | 19 -
.../algorithms/alignment/sdp/FragmentSortImpl.hpp | 16 -
.../sdp/NonoverlappingSparseDynamicProgramming.h | 193 -
.../algorithms/alignment/sdp/SDPColumn.hpp | 23 -
.../algorithms/alignment/sdp/SDPFragment.cpp | 27 -
.../algorithms/alignment/sdp/SDPFragment.hpp | 132 -
.../alignment/algorithms/alignment/sdp/SDPSet.hpp | 52 -
.../algorithms/alignment/sdp/SDPSetImpl.hpp | 113 -
.../alignment/sdp/SparseDynamicProgramming.cpp | 18 -
.../alignment/sdp/SparseDynamicProgramming.hpp | 37 -
.../alignment/sdp/SparseDynamicProgrammingImpl.hpp | 266 -
.../alignment/sdp/VariableLengthSDPFragment.h | 51 -
.../alignment/algorithms/anchoring/BWTSearch.cpp | 85 -
.../alignment/algorithms/anchoring/BWTSearch.hpp | 35 -
.../algorithms/anchoring/BWTSearchImpl.hpp | 14 -
.../algorithms/anchoring/BasicEndpoint.hpp | 50 -
.../algorithms/anchoring/BasicEndpointImpl.hpp | 78 -
.../algorithms/anchoring/ClusterProbability.cpp | 45 -
.../algorithms/anchoring/ClusterProbability.hpp | 13 -
.../alignment/algorithms/anchoring/Coordinate.cpp | 12 -
.../alignment/algorithms/anchoring/Coordinate.hpp | 45 -
.../algorithms/anchoring/FindMaxInterval.cpp | 23 -
.../algorithms/anchoring/FindMaxInterval.hpp | 175 -
.../algorithms/anchoring/FindMaxIntervalImpl.hpp | 945 -
.../alignment/algorithms/anchoring/GlobalChain.hpp | 37 -
.../algorithms/anchoring/GlobalChainImpl.hpp | 225 -
.../alignment/algorithms/anchoring/LISPValue.hpp | 24 -
.../algorithms/anchoring/LISPValueImpl.hpp | 165 -
.../algorithms/anchoring/LISPValueWeightor.hpp | 52 -
.../algorithms/anchoring/LISPValueWeightorImpl.hpp | 112 -
.../algorithms/anchoring/LISQValueWeightor.hpp | 35 -
.../algorithms/anchoring/LISSizeWeightor.hpp | 14 -
.../algorithms/anchoring/LISSizeWeightorImpl.hpp | 13 -
.../anchoring/LongestIncreasingSubsequence.hpp | 31 -
.../anchoring/LongestIncreasingSubsequenceImpl.hpp | 135 -
.../algorithms/anchoring/MapBySuffixArray.hpp | 44 -
.../algorithms/anchoring/MapBySuffixArrayImpl.hpp | 315 -
.../algorithms/anchoring/PrioritySearchTree.hpp | 69 -
.../anchoring/PrioritySearchTreeImpl.hpp | 296 -
.../algorithms/anchoring/ScoreAnchors.hpp | 46 -
.../algorithms/anchoring/ScoreAnchorsImpl.hpp | 179 -
.../algorithms/compare/CompareStrings.hpp | 81 -
.../algorithms/sorting/DifferenceCovers.cpp | 15 -
.../algorithms/sorting/DifferenceCovers.hpp | 16 -
libcpp/alignment/algorithms/sorting/Karkkainen.hpp | 134 -
.../algorithms/sorting/LightweightSuffixArray.cpp | 405 -
.../algorithms/sorting/LightweightSuffixArray.hpp | 103 -
.../algorithms/sorting/MultikeyQuicksort.cpp | 197 -
.../algorithms/sorting/MultikeyQuicksort.hpp | 48 -
libcpp/alignment/algorithms/sorting/qsufsort.cpp | 302 -
libcpp/alignment/algorithms/sorting/qsufsort.hpp | 376 -
libcpp/alignment/anchoring/AnchorParameters.hpp | 35 -
libcpp/alignment/build.mk | 1 -
libcpp/alignment/bwt/BWT.hpp | 316 -
libcpp/alignment/bwt/Occ.hpp | 217 -
libcpp/alignment/bwt/PackedHash.hpp | 350 -
libcpp/alignment/bwt/Pos.hpp | 47 -
.../datastructures/alignment/AlignedPair.h | 19 -
.../datastructures/alignment/Alignment.cpp | 512 -
.../datastructures/alignment/Alignment.hpp | 184 -
.../alignment/AlignmentCandidate.cpp | 26 -
.../alignment/AlignmentCandidate.hpp | 370 -
.../datastructures/alignment/AlignmentContext.cpp | 35 -
.../datastructures/alignment/AlignmentContext.hpp | 32 -
.../datastructures/alignment/AlignmentGapList.h | 26 -
.../datastructures/alignment/AlignmentMap.cpp | 22 -
.../datastructures/alignment/AlignmentMap.hpp | 20 -
.../datastructures/alignment/AlignmentStats.cpp | 29 -
.../datastructures/alignment/AlignmentStats.hpp | 25 -
.../datastructures/alignment/ByteAlignment.h | 347 -
.../alignment/datastructures/alignment/CmpFile.cpp | 6 -
.../alignment/datastructures/alignment/CmpFile.hpp | 33 -
.../alignment/CmpIndexedStringTable.h | 67 -
.../datastructures/alignment/CmpReadGroupTable.h | 22 -
.../datastructures/alignment/CmpRefSeqTable.h | 22 -
.../datastructures/alignment/FilterCriteria.cpp | 371 -
.../datastructures/alignment/FilterCriteria.hpp | 165 -
libcpp/alignment/datastructures/alignment/Path.h | 23 -
.../alignment/SAMToAlignmentCandidateAdapter.cpp | 461 -
.../alignment/SAMToAlignmentCandidateAdapter.hpp | 79 -
.../alignmentset/AlignmentSetToCmpH5Adapter.hpp | 84 -
.../AlignmentSetToCmpH5AdapterImpl.hpp | 256 -
.../alignmentset/SAMQVConversion.cpp | 27 -
.../alignmentset/SAMQVConversion.hpp | 15 -
.../alignmentset/SAMSupplementalQVList.cpp | 71 -
.../alignmentset/SAMSupplementalQVList.hpp | 27 -
.../datastructures/anchoring/AnchorParameters.cpp | 44 -
.../datastructures/anchoring/AnchorParameters.hpp | 35 -
.../datastructures/anchoring/ClusterList.cpp | 75 -
.../datastructures/anchoring/ClusterList.hpp | 25 -
.../datastructures/anchoring/MatchPos.cpp | 59 -
.../datastructures/anchoring/MatchPos.hpp | 192 -
.../datastructures/anchoring/WeightedInterval.cpp | 181 -
.../datastructures/anchoring/WeightedInterval.hpp | 85 -
libcpp/alignment/files/BaseSequenceIO.cpp | 77 -
libcpp/alignment/files/BaseSequenceIO.hpp | 26 -
libcpp/alignment/files/CCSIterator.cpp | 28 -
libcpp/alignment/files/CCSIterator.hpp | 21 -
libcpp/alignment/files/FragmentCCSIterator.cpp | 109 -
libcpp/alignment/files/FragmentCCSIterator.hpp | 23 -
libcpp/alignment/files/ReaderAgglomerate.cpp | 505 -
libcpp/alignment/files/ReaderAgglomerate.hpp | 136 -
libcpp/alignment/files/ReaderAgglomerateImpl.hpp | 44 -
libcpp/alignment/format/BAMPrinter.hpp | 29 -
libcpp/alignment/format/BAMPrinterImpl.hpp | 168 -
.../alignment/format/CompareSequencesPrinter.cpp | 10 -
.../alignment/format/CompareSequencesPrinter.hpp | 21 -
.../format/CompareSequencesPrinterImpl.hpp | 77 -
libcpp/alignment/format/IntervalPrinter.cpp | 70 -
libcpp/alignment/format/IntervalPrinter.hpp | 21 -
libcpp/alignment/format/SAMHeaderPrinter.cpp | 432 -
libcpp/alignment/format/SAMHeaderPrinter.hpp | 311 -
libcpp/alignment/format/SAMPrinter.cpp | 188 -
libcpp/alignment/format/SAMPrinter.hpp | 93 -
libcpp/alignment/format/SAMPrinterImpl.hpp | 304 -
libcpp/alignment/format/StickAlignmentPrinter.hpp | 123 -
libcpp/alignment/format/SummaryPrinter.cpp | 26 -
libcpp/alignment/format/SummaryPrinter.hpp | 14 -
libcpp/alignment/format/VulgarPrinter.hpp | 53 -
libcpp/alignment/format/XMLPrinter.hpp | 84 -
libcpp/alignment/ipc/SharedMemoryAllocator.hpp | 33 -
libcpp/alignment/makefile | 52 -
libcpp/alignment/old.Makefile | 113 -
libcpp/alignment/qvs/QualityValueProfile.cpp | 41 -
libcpp/alignment/qvs/QualityValueProfile.hpp | 23 -
libcpp/alignment/simulator/CDFMap.hpp | 44 -
libcpp/alignment/simulator/ContextOutputList.hpp | 100 -
libcpp/alignment/simulator/ContextSample.cpp | 53 -
libcpp/alignment/simulator/ContextSample.hpp | 30 -
libcpp/alignment/simulator/ContextSet.cpp | 35 -
libcpp/alignment/simulator/ContextSet.hpp | 19 -
libcpp/alignment/simulator/LengthHistogram.cpp | 58 -
libcpp/alignment/simulator/LengthHistogram.hpp | 24 -
libcpp/alignment/simulator/OutputList.hpp | 57 -
libcpp/alignment/simulator/OutputSample.hpp | 59 -
libcpp/alignment/simulator/OutputSampleList.hpp | 33 -
libcpp/alignment/simulator/OutputSampleListSet.hpp | 123 -
libcpp/alignment/simulator/QualitySample.cpp | 77 -
libcpp/alignment/simulator/QualitySample.hpp | 28 -
.../statistics/AnchorDistributionTable.hpp | 43518 -------------------
.../statistics/LookupAnchorDistribution.cpp | 58 -
.../statistics/LookupAnchorDistribution.hpp | 10 -
libcpp/alignment/statistics/StatUtils.cpp | 45 -
libcpp/alignment/statistics/StatUtils.hpp | 165 -
libcpp/alignment/statistics/StatUtilsImpl.hpp | 57 -
.../alignment/statistics/VarianceAccumulator.hpp | 28 -
.../statistics/VarianceAccumulatorImpl.hpp | 60 -
libcpp/alignment/statistics/cdfs.cpp | 53 -
libcpp/alignment/statistics/cdfs.hpp | 418 -
libcpp/alignment/statistics/pdfs.cpp | 36 -
libcpp/alignment/statistics/pdfs.hpp | 18 -
libcpp/alignment/suffixarray/LCPTable.hpp | 182 -
libcpp/alignment/suffixarray/SharedSuffixArray.hpp | 83 -
libcpp/alignment/suffixarray/SuffixArray.hpp | 1197 -
libcpp/alignment/suffixarray/SuffixArrayTypes.hpp | 17 -
libcpp/alignment/suffixarray/ssort.hpp | 449 -
libcpp/alignment/tuples/BaseTuple.cpp | 53 -
libcpp/alignment/tuples/BaseTuple.hpp | 27 -
libcpp/alignment/tuples/CompressedDNATuple.hpp | 63 -
libcpp/alignment/tuples/CountedTuple.h | 16 -
libcpp/alignment/tuples/DNATuple.cpp | 94 -
libcpp/alignment/tuples/DNATuple.hpp | 103 -
libcpp/alignment/tuples/DNATupleImpl.hpp | 200 -
libcpp/alignment/tuples/DNATupleList.h | 53 -
libcpp/alignment/tuples/HashedTupleList.hpp | 61 -
libcpp/alignment/tuples/HashedTupleListImpl.hpp | 144 -
libcpp/alignment/tuples/TupleCountTable.hpp | 33 -
libcpp/alignment/tuples/TupleCountTableImpl.hpp | 101 -
libcpp/alignment/tuples/TupleList.hpp | 64 -
libcpp/alignment/tuples/TupleListImpl.hpp | 134 -
libcpp/alignment/tuples/TupleMask.h | 13 -
libcpp/alignment/tuples/TupleMatching.hpp | 25 -
libcpp/alignment/tuples/TupleMatchingImpl.hpp | 106 -
libcpp/alignment/tuples/TupleMetrics.cpp | 16 -
libcpp/alignment/tuples/TupleMetrics.hpp | 19 -
libcpp/alignment/tuples/TupleOperations.h | 7 -
libcpp/alignment/tuples/TupleTranslations.h | 4 -
libcpp/alignment/tuples/tuple.h | 82 -
libcpp/alignment/utils/FileOfFileNames.cpp | 102 -
libcpp/alignment/utils/FileOfFileNames.hpp | 27 -
libcpp/alignment/utils/FileUtils.cpp | 61 -
libcpp/alignment/utils/FileUtils.hpp | 27 -
libcpp/alignment/utils/LogUtils.cpp | 55 -
libcpp/alignment/utils/LogUtils.hpp | 15 -
libcpp/alignment/utils/PhredUtils.cpp | 13 -
libcpp/alignment/utils/PhredUtils.hpp | 8 -
libcpp/alignment/utils/RangeUtils.cpp | 107 -
libcpp/alignment/utils/RangeUtils.hpp | 56 -
libcpp/alignment/utils/RegionUtils.cpp | 302 -
libcpp/alignment/utils/RegionUtils.hpp | 132 -
libcpp/alignment/utils/RegionUtilsImpl.hpp | 215 -
libcpp/alignment/utils/SimpleXMLUtils.hpp | 99 -
libcpp/alignment/utils/TimeUtils.cpp | 20 -
libcpp/alignment/utils/TimeUtils.hpp | 7 -
libcpp/configure.py | 268 -
libcpp/hdf/BufferedHDF2DArray.cpp | 79 -
libcpp/hdf/BufferedHDF2DArray.hpp | 158 -
libcpp/hdf/BufferedHDF2DArrayImpl.hpp | 379 -
libcpp/hdf/BufferedHDFArray.cpp | 92 -
libcpp/hdf/BufferedHDFArray.hpp | 207 -
libcpp/hdf/BufferedHDFArrayImpl.hpp | 435 -
libcpp/hdf/DatasetCollection.cpp | 61 -
libcpp/hdf/DatasetCollection.hpp | 41 -
libcpp/hdf/DatasetCollectionImpl.hpp | 29 -
libcpp/hdf/HDF2DArray.hpp | 25 -
libcpp/hdf/HDFAlnGroup.hpp | 50 -
libcpp/hdf/HDFAlnGroupGroup.cpp | 52 -
libcpp/hdf/HDFAlnGroupGroup.hpp | 27 -
libcpp/hdf/HDFAlnInfoGroup.cpp | 102 -
libcpp/hdf/HDFAlnInfoGroup.hpp | 46 -
libcpp/hdf/HDFArray.hpp | 85 -
libcpp/hdf/HDFAtom.cpp | 159 -
libcpp/hdf/HDFAtom.hpp | 176 -
libcpp/hdf/HDFAttributable.cpp | 41 -
libcpp/hdf/HDFAttributable.hpp | 23 -
libcpp/hdf/HDFBasReader.cpp | 46 -
libcpp/hdf/HDFBasReader.hpp | 1178 -
libcpp/hdf/HDFBasWriter.hpp | 390 -
libcpp/hdf/HDFCCSReader.hpp | 257 -
libcpp/hdf/HDFCmpData.hpp | 36 -
libcpp/hdf/HDFCmpExperimentGroup.cpp | 193 -
libcpp/hdf/HDFCmpExperimentGroup.hpp | 70 -
libcpp/hdf/HDFCmpFile.hpp | 844 -
libcpp/hdf/HDFCmpReader.hpp | 663 -
libcpp/hdf/HDFCmpRefAlignmentGroup.hpp | 102 -
libcpp/hdf/HDFCmpRootGroup.hpp | 66 -
libcpp/hdf/HDFCmpSupportedFields.cpp | 25 -
libcpp/hdf/HDFCmpSupportedFields.hpp | 13 -
libcpp/hdf/HDFCommonFG.hpp | 13 -
libcpp/hdf/HDFConfig.hpp | 7 -
libcpp/hdf/HDFData.cpp | 74 -
libcpp/hdf/HDFData.hpp | 52 -
libcpp/hdf/HDFFile.cpp | 53 -
libcpp/hdf/HDFFile.hpp | 32 -
libcpp/hdf/HDFFileLogGroup.hpp | 55 -
libcpp/hdf/HDFGroup.cpp | 58 -
libcpp/hdf/HDFGroup.hpp | 36 -
libcpp/hdf/HDFMovieInfoGroup.hpp | 79 -
libcpp/hdf/HDFNewBasReader.cpp | 72 -
libcpp/hdf/HDFNewBasReader.hpp | 39 -
libcpp/hdf/HDFPlsReader.hpp | 542 -
libcpp/hdf/HDFPlsWriter.hpp | 195 -
libcpp/hdf/HDFPulseDataFile.cpp | 151 -
libcpp/hdf/HDFPulseDataFile.hpp | 67 -
libcpp/hdf/HDFRefGroupGroup.hpp | 65 -
libcpp/hdf/HDFRefInfoGroup.hpp | 84 -
libcpp/hdf/HDFRegionTableReader.cpp | 149 -
libcpp/hdf/HDFRegionTableReader.hpp | 47 -
libcpp/hdf/HDFRegionTableWriter.hpp | 140 -
libcpp/hdf/HDFSMRTSequenceReader.hpp | 71 -
libcpp/hdf/HDFScanDataReader.cpp | 262 -
libcpp/hdf/HDFScanDataReader.hpp | 101 -
libcpp/hdf/HDFScanDataWriter.cpp | 164 -
libcpp/hdf/HDFScanDataWriter.hpp | 71 -
libcpp/hdf/HDFSentinalFile.hpp | 21 -
libcpp/hdf/HDFUtils.cpp | 82 -
libcpp/hdf/HDFUtils.hpp | 44 -
libcpp/hdf/HDFWriteBuffer.hpp | 52 -
libcpp/hdf/HDFZMWReader.cpp | 136 -
libcpp/hdf/HDFZMWReader.hpp | 45 -
libcpp/hdf/build.mk | 1 -
libcpp/hdf/makefile | 28 -
libcpp/hdf/old.Makefile | 94 -
libcpp/makefile | 32 -
libcpp/old.Makefile | 28 -
libcpp/pbdata/.gitignore | 2 -
libcpp/pbdata/CCSSequence.cpp | 35 -
libcpp/pbdata/CCSSequence.hpp | 43 -
libcpp/pbdata/ChangeListID.cpp | 64 -
libcpp/pbdata/ChangeListID.hpp | 38 -
libcpp/pbdata/CommandLineParser.cpp | 846 -
libcpp/pbdata/CommandLineParser.hpp | 175 -
libcpp/pbdata/Compare4BitCompressed.hpp | 98 -
libcpp/pbdata/CompressedDNASequence.hpp | 89 -
libcpp/pbdata/CompressedSequence.hpp | 100 -
libcpp/pbdata/CompressedSequenceImpl.hpp | 343 -
libcpp/pbdata/DNASequence.cpp | 402 -
libcpp/pbdata/DNASequence.hpp | 183 -
libcpp/pbdata/Enumerations.h | 39 -
libcpp/pbdata/FASTAReader.cpp | 420 -
libcpp/pbdata/FASTAReader.hpp | 80 -
libcpp/pbdata/FASTASequence.cpp | 246 -
libcpp/pbdata/FASTASequence.hpp | 91 -
libcpp/pbdata/FASTQReader.cpp | 89 -
libcpp/pbdata/FASTQReader.hpp | 24 -
libcpp/pbdata/FASTQSequence.cpp | 651 -
libcpp/pbdata/FASTQSequence.hpp | 146 -
libcpp/pbdata/GFFFile.cpp | 39 -
libcpp/pbdata/GFFFile.hpp | 33 -
libcpp/pbdata/MD5Utils.cpp | 464 -
libcpp/pbdata/MD5Utils.hpp | 113 -
libcpp/pbdata/MD5UtilsImpl.hpp | 57 -
libcpp/pbdata/NucConversion.cpp | 409 -
libcpp/pbdata/NucConversion.hpp | 50 -
libcpp/pbdata/PackedDNASequence.cpp | 233 -
libcpp/pbdata/PackedDNASequence.hpp | 60 -
libcpp/pbdata/ReverseCompressIndex.cpp | 40 -
libcpp/pbdata/ReverseCompressIndex.hpp | 25 -
libcpp/pbdata/SMRTSequence.cpp | 283 -
libcpp/pbdata/SMRTSequence.hpp | 115 -
libcpp/pbdata/SeqUtils.hpp | 17 -
libcpp/pbdata/SeqUtilsImpl.hpp | 47 -
libcpp/pbdata/StringUtils.cpp | 133 -
libcpp/pbdata/StringUtils.hpp | 71 -
libcpp/pbdata/Types.h | 21 -
libcpp/pbdata/VectorUtils.hpp | 17 -
libcpp/pbdata/alignment/CmpAlignment.cpp | 219 -
libcpp/pbdata/alignment/CmpAlignment.hpp | 126 -
libcpp/pbdata/alignment/CmpAlignmentImpl.hpp | 6 -
libcpp/pbdata/amos/AfgBasWriter.cpp | 102 -
libcpp/pbdata/amos/AfgBasWriter.hpp | 59 -
libcpp/pbdata/build.mk | 1 -
libcpp/pbdata/defs.h | 19 -
libcpp/pbdata/loadpulses/MetricField.cpp | 87 -
libcpp/pbdata/loadpulses/MetricField.hpp | 115 -
.../pbdata/loadpulses/MovieAlnIndexLookupTable.cpp | 54 -
.../pbdata/loadpulses/MovieAlnIndexLookupTable.hpp | 117 -
libcpp/pbdata/makefile | 40 -
libcpp/pbdata/matrix/FlatMatrix.hpp | 98 -
libcpp/pbdata/matrix/FlatMatrixImpl.hpp | 192 -
libcpp/pbdata/matrix/Matrix.hpp | 50 -
libcpp/pbdata/matrix/MatrixImpl.hpp | 117 -
libcpp/pbdata/metagenome/FindRandomSequence.hpp | 70 -
libcpp/pbdata/metagenome/SequenceIndexDatabase.hpp | 96 -
.../metagenome/SequenceIndexDatabaseImpl.hpp | 347 -
libcpp/pbdata/metagenome/TitleTable.cpp | 109 -
libcpp/pbdata/metagenome/TitleTable.hpp | 39 -
libcpp/pbdata/mklibconfig.sh | 32 -
libcpp/pbdata/old.Makefile | 87 -
libcpp/pbdata/qvs/QualityTransform.cpp | 23 -
libcpp/pbdata/qvs/QualityTransform.hpp | 26 -
libcpp/pbdata/qvs/QualityValue.cpp | 65 -
libcpp/pbdata/qvs/QualityValue.hpp | 31 -
libcpp/pbdata/qvs/QualityValueVector.hpp | 47 -
libcpp/pbdata/qvs/QualityValueVectorImpl.hpp | 99 -
libcpp/pbdata/reads/BaseFile.cpp | 82 -
libcpp/pbdata/reads/BaseFile.hpp | 49 -
libcpp/pbdata/reads/BaseFileImpl.hpp | 11 -
libcpp/pbdata/reads/HoleXY.cpp | 14 -
libcpp/pbdata/reads/HoleXY.hpp | 14 -
libcpp/pbdata/reads/PulseBaseCommon.cpp | 37 -
libcpp/pbdata/reads/PulseBaseCommon.hpp | 26 -
libcpp/pbdata/reads/PulseFile.cpp | 76 -
libcpp/pbdata/reads/PulseFile.hpp | 53 -
libcpp/pbdata/reads/PulseFileImpl.hpp | 21 -
libcpp/pbdata/reads/ReadInterval.hpp | 18 -
libcpp/pbdata/reads/ReadType.cpp | 43 -
libcpp/pbdata/reads/ReadType.hpp | 18 -
libcpp/pbdata/reads/RegionTable.cpp | 159 -
libcpp/pbdata/reads/RegionTable.hpp | 95 -
libcpp/pbdata/reads/ScanData.cpp | 12 -
libcpp/pbdata/reads/ScanData.hpp | 20 -
libcpp/pbdata/reads/ZMWGroupEntry.cpp | 8 -
libcpp/pbdata/reads/ZMWGroupEntry.hpp | 17 -
libcpp/pbdata/saf/AlnGroup.cpp | 12 -
libcpp/pbdata/saf/AlnGroup.hpp | 14 -
libcpp/pbdata/saf/AlnInfo.hpp | 17 -
libcpp/pbdata/saf/MovieInfo.cpp | 13 -
libcpp/pbdata/saf/MovieInfo.hpp | 19 -
libcpp/pbdata/saf/RefGroup.cpp | 25 -
libcpp/pbdata/saf/RefGroup.hpp | 21 -
libcpp/pbdata/saf/RefInfo.cpp | 20 -
libcpp/pbdata/saf/RefInfo.hpp | 26 -
libcpp/pbdata/sam/AlignmentSet.hpp | 31 -
libcpp/pbdata/sam/AlignmentSetImpl.hpp | 31 -
libcpp/pbdata/sam/CigarString.h | 23 -
libcpp/pbdata/sam/ReadGroup.cpp | 51 -
libcpp/pbdata/sam/ReadGroup.hpp | 40 -
libcpp/pbdata/sam/ReferenceSequence.cpp | 47 -
libcpp/pbdata/sam/ReferenceSequence.hpp | 72 -
libcpp/pbdata/sam/SAMAlignment.cpp | 199 -
libcpp/pbdata/sam/SAMAlignment.hpp | 97 -
libcpp/pbdata/sam/SAMFlag.h | 48 -
libcpp/pbdata/sam/SAMHeader.cpp | 31 -
libcpp/pbdata/sam/SAMHeader.hpp | 18 -
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