[med-svn] [pbseqlib] 03/04: Merge tag 'upstream/0_20151014+gitbe5d1bf'
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sat Oct 17 08:32:07 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository pbseqlib.
commit 4dcaffe5f428325eb8f80a87e24461766310465f
Merge: 011a4f9 4bf6973
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Oct 15 23:28:04 2015 -0700
Merge tag 'upstream/0_20151014+gitbe5d1bf'
Upstream version 0~20151014+gitbe5d1bf
.gitignore | 9 +-
.travis.yml | 6 +-
Makefile | 36 ---
README.md | 24 +-
alignment/Makefile | 113 -------
.../algorithms/anchoring/MapBySuffixArrayImpl.hpp | 20 +-
alignment/algorithms/sorting/DifferenceCovers.cpp | 3 +-
.../algorithms/sorting/LightweightSuffixArray.cpp | 11 +-
alignment/algorithms/sorting/MultikeyQuicksort.cpp | 2 +-
alignment/algorithms/sorting/qsufsort.hpp | 5 +-
alignment/build.mk | 1 +
alignment/bwt/Occ.hpp | 2 +-
alignment/bwt/PackedHash.hpp | 14 +-
.../datastructures/alignment/FilterCriteria.cpp | 2 +
alignment/files/FragmentCCSIterator.cpp | 3 +-
alignment/files/ReaderAgglomerate.cpp | 52 +++-
alignment/files/ReaderAgglomerate.hpp | 4 +
alignment/format/BAMPrinter.hpp | 18 +-
alignment/format/BAMPrinterImpl.hpp | 67 +++-
alignment/format/SAMHeaderPrinter.cpp | 25 +-
alignment/format/SAMPrinter.cpp | 7 +-
alignment/format/SAMPrinter.hpp | 1 +
alignment/format/SAMPrinterImpl.hpp | 14 +-
alignment/makefile | 47 +++
alignment/simple.mk | 82 -----
alignment/simulator/ContextOutputList.hpp | 2 +-
alignment/simulator/ContextSet.cpp | 4 +-
alignment/simulator/OutputSampleListSet.hpp | 3 +-
alignment/suffixarray/LCPTable.hpp | 21 +-
alignment/suffixarray/SuffixArray.hpp | 1 -
alignment/suffixarray/ssort.hpp | 6 +-
alignment/tuples/TupleCountTableImpl.hpp | 5 +-
alignment/tuples/TupleListImpl.hpp | 1 -
alignment/utils/RegionUtils.cpp | 111 +------
alignment/utils/RegionUtils.hpp | 48 ---
alignment/utils/RegionUtilsImpl.hpp | 231 +++-----------
common.mk | 84 -----
configure.py | 339 +++++++++++++++++++++
hdf/BufferedHDF2DArrayImpl.hpp | 15 +-
hdf/BufferedHDFArrayImpl.hpp | 3 +-
hdf/HDFAtom.cpp | 9 +-
hdf/HDFAtom.hpp | 37 ++-
hdf/HDFAttributable.cpp | 6 +-
hdf/HDFAttributable.hpp | 4 +-
hdf/HDFBasReader.hpp | 240 ++++++++-------
hdf/HDFBaseCallsWriter.cpp | 326 ++++++++++++++++++++
hdf/HDFBaseCallsWriter.hpp | 233 ++++++++++++++
hdf/HDFBaxWriter.cpp | 141 +++++++++
hdf/HDFBaxWriter.hpp | 172 +++++++++++
hdf/HDFCmpFile.hpp | 14 +-
hdf/HDFCmpReader.hpp | 1 +
hdf/HDFCmpRefAlignmentGroup.hpp | 3 +-
hdf/HDFData.cpp | 10 +-
hdf/HDFData.hpp | 10 +-
hdf/HDFPlsReader.hpp | 16 +-
hdf/HDFRegionTableReader.cpp | 115 ++++---
hdf/HDFRegionTableReader.hpp | 30 +-
hdf/HDFRegionsWriter.cpp | 99 ++++++
hdf/HDFRegionsWriter.hpp | 101 ++++++
hdf/HDFScanDataReader.cpp | 29 +-
hdf/HDFScanDataReader.hpp | 7 +-
hdf/HDFScanDataWriter.cpp | 127 +++++---
hdf/HDFScanDataWriter.hpp | 55 +++-
hdf/HDFWriteBuffer.hpp | 3 +-
hdf/HDFWriterBase.cpp | 98 ++++++
hdf/HDFWriterBase.hpp | 88 ++++++
hdf/HDFZMWMetricsWriter.cpp | 142 +++++++++
hdf/HDFZMWMetricsWriter.hpp | 117 +++++++
hdf/HDFZMWWriter.cpp | 144 +++++++++
hdf/HDFZMWWriter.hpp | 120 ++++++++
hdf/Makefile | 94 ------
hdf/build.mk | 1 +
hdf/makefile | 33 ++
makefile | 31 ++
pbdata/.gitignore | 2 +
pbdata/CCSSequence.cpp | 21 +-
pbdata/CCSSequence.hpp | 22 +-
pbdata/CompressedDNASequence.hpp | 6 +-
pbdata/CompressedSequenceImpl.hpp | 13 +-
pbdata/DNASequence.cpp | 30 +-
pbdata/DNASequence.hpp | 15 +-
pbdata/Enumerations.h | 47 ++-
pbdata/FASTAReader.cpp | 11 +-
pbdata/FASTASequence.cpp | 38 +--
pbdata/FASTASequence.hpp | 16 +-
pbdata/FASTQReader.cpp | 2 +-
pbdata/FASTQSequence.cpp | 50 ++-
pbdata/FASTQSequence.hpp | 41 ++-
pbdata/MD5Utils.cpp | 5 +-
pbdata/Makefile | 85 ------
pbdata/PacBioDefs.h | 180 +++++++++++
pbdata/PackedDNASequence.cpp | 6 +-
pbdata/ReverseCompressIndex.cpp | 3 +-
pbdata/SMRTSequence.cpp | 289 +++++++++++++-----
pbdata/SMRTSequence.hpp | 161 +++++++---
pbdata/StringUtils.cpp | 52 +---
pbdata/StringUtils.hpp | 2 +-
pbdata/build.mk | 1 +
pbdata/makefile | 39 +++
pbdata/matrix/FlatMatrixImpl.hpp | 9 +-
pbdata/matrix/MatrixImpl.hpp | 7 +-
pbdata/metagenome/SequenceIndexDatabaseImpl.hpp | 16 +-
pbdata/metagenome/TitleTable.cpp | 10 +-
pbdata/reads/BaseFile.cpp | 6 +-
pbdata/reads/PulseBaseCommon.cpp | 39 ++-
pbdata/reads/PulseBaseCommon.hpp | 39 ++-
pbdata/reads/PulseFile.cpp | 40 ++-
pbdata/reads/PulseFileImpl.hpp | 4 +-
pbdata/reads/ReadInterval.hpp | 19 +-
pbdata/reads/RegionAnnotation.cpp | 49 +++
pbdata/reads/RegionAnnotation.hpp | 241 +++++++++++++++
pbdata/reads/RegionAnnotations.cpp | 179 +++++++++++
pbdata/reads/RegionAnnotations.hpp | 122 ++++++++
pbdata/reads/RegionTable.cpp | 239 +++++++--------
pbdata/reads/RegionTable.hpp | 166 ++++++----
pbdata/reads/RegionTypeMap.cpp | 89 ++++++
pbdata/reads/RegionTypeMap.hpp | 85 ++++++
pbdata/reads/ScanData.cpp | 155 +++++++++-
pbdata/reads/ScanData.hpp | 86 +++++-
pbdata/sam/SAMReaderImpl.hpp | 2 +-
pbdata/utils.hpp | 5 +-
pbdata/utils/SMRTReadUtils.cpp | 4 +-
pbdata/utils/SMRTTitle.hpp | 14 +
pbdata/utilsImpl.hpp | 32 +-
rules.mk | 28 ++
simple.mk | 16 -
travis.sh | 14 +
unittest/.gitignore | 1 +
unittest/Makefile | 41 ---
unittest/alignment/Makefile | 9 +-
unittest/alignment/files/CCSIterator_gtest.cpp | 2 -
.../alignment/files/FragmentCCSIterator_gtest.cpp | 5 +-
.../files/FragmentCCSIterator_other_gtest.cpp | 100 ++++++
.../alignment/files/ReaderAgglomerate_gtest.cpp | 16 +
unittest/alignment/utils/RegionUtils_gtest.cpp | 1 -
unittest/build.mk | 27 ++
unittest/common.mk | 64 ----
unittest/hdf/HDFPlsReader_gtest.cpp | 3 +-
unittest/hdf/HDFScanDataWriter_gtest.cpp | 2 +
unittest/hdf/Makefile | 9 +-
unittest/makefile | 120 ++++++++
unittest/pbdata/CCSSequence_gtest.cpp | 8 +-
unittest/pbdata/DNASequence_gtest.cpp | 2 +-
unittest/pbdata/Makefile | 9 +-
unittest/pbdata/SMRTSequence_gtest.cpp | 6 +-
unittest/pbdata/StringUtils_gtest.cpp | 44 ++-
unittest/pbdata/reads/RegionAnnotations_gtest.cpp | 203 ++++++++++++
unittest/pbdata/reads/RegionTypeMap_gtest.cpp | 61 ++++
148 files changed, 5744 insertions(+), 1939 deletions(-)
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