[med-svn] [blasr] 04/12: Merge tag 'upstream/0_20150925+git77862af'
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Dec 14 21:14:43 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository blasr.
commit 71819370d7ad50aedd34d7f9e280a2046e43d0d5
Merge: df881fc 255f617
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Dec 12 21:30:21 2015 -0800
Merge tag 'upstream/0_20150925+git77862af'
Upstream version 0~20150925+git77862af
.gitignore | 4 +
Blasr.cpp | 34 +
MANUAL.md | 84 -
Makefile | 59 -
README.INSTALL.md | 72 +
README.MANUAL.md | 38 +
README.md | 52 +-
blasr_git_common.mk | 15 -
blasr_gitp4.mk | 24 -
common.mk | 139 -
configure.py | 104 +-
ctest/hitpolicy.t | 14 +-
ctest/useccsallLargeGenome.t | 3 +-
extrautils/GNUmakefile | 45 -
extrautils/Makefile | 78 -
extrautils/makefile | 49 +
extrautils/p4.mk | 79 -
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 -
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.../algorithms/alignment/AlignmentUtils.hpp | 139 -
.../algorithms/alignment/AlignmentUtilsImpl.hpp | 548 -
.../algorithms/alignment/BaseScoreFunction.cpp | 11 -
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.../alignment/DistanceMatrixScoreFunction.hpp | 40 -
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.../algorithms/alignment/OneGapAlignment.hpp | 374 -
.../alignment/QualityValueScoreFunction.cpp | 90 -
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libcpp/alignment/algorithms/alignment/SDPAlign.hpp | 64 -
.../algorithms/alignment/SDPAlignImpl.hpp | 614 -
libcpp/alignment/algorithms/alignment/SWAlign.hpp | 17 -
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.../algorithms/compare/CompareStrings.hpp | 81 -
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libcpp/alignment/algorithms/sorting/Karkkainen.hpp | 134 -
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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 -
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.../datastructures/alignment/AlignmentContext.cpp | 35 -
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libcpp/alignment/datastructures/alignment/Path.h | 23 -
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.../datastructures/anchoring/WeightedInterval.cpp | 181 -
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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 -
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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 -
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libcpp/alignment/statistics/StatUtils.cpp | 45 -
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libcpp/alignment/statistics/cdfs.cpp | 53 -
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libcpp/alignment/statistics/pdfs.cpp | 36 -
libcpp/alignment/statistics/pdfs.hpp | 18 -
libcpp/alignment/suffixarray/LCPTable.hpp | 182 -
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libcpp/alignment/tuples/BaseTuple.cpp | 53 -
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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 -
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libcpp/alignment/tuples/TupleMask.h | 13 -
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libcpp/alignment/tuples/TupleOperations.h | 7 -
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libcpp/alignment/utils/FileOfFileNames.cpp | 102 -
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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 -
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libcpp/hdf/HDFCmpFile.hpp | 844 -
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libcpp/hdf/HDFCmpSupportedFields.cpp | 25 -
libcpp/hdf/HDFCmpSupportedFields.hpp | 13 -
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libcpp/hdf/HDFConfig.hpp | 7 -
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libcpp/hdf/HDFMovieInfoGroup.hpp | 79 -
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libcpp/hdf/HDFPlsReader.hpp | 542 -
libcpp/hdf/HDFPlsWriter.hpp | 195 -
libcpp/hdf/HDFPulseDataFile.cpp | 151 -
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libcpp/hdf/HDFRefGroupGroup.hpp | 65 -
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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 -
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libcpp/pbdata/Compare4BitCompressed.hpp | 98 -
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libcpp/pbdata/FASTAReader.cpp | 420 -
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libcpp/pbdata/sam/SAMAlignment.cpp | 199 -
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.../unittest/alignment/utils/RangeUtils_gtest.cpp | 63 -
.../unittest/alignment/utils/RegionUtils_gtest.cpp | 236 -
libcpp/unittest/build.mk | 27 -
libcpp/unittest/common.mk | 64 -
libcpp/unittest/hdf/HDF2DArray_gtest.cpp | 96 -
libcpp/unittest/hdf/HDFBasReader_gtest.cpp | 56 -
libcpp/unittest/hdf/HDFCCSReader_gtest.cpp | 68 -
libcpp/unittest/hdf/HDFPlsReader_gtest.cpp | 49 -
libcpp/unittest/hdf/HDFScanDataReader_gtest.cpp | 52 -
libcpp/unittest/hdf/HDFScanDataWriter_gtest.cpp | 36 -
libcpp/unittest/hdf/HDFUtils_gtest.cpp | 38 -
libcpp/unittest/hdf/HDFZMWReader_gtest.cpp | 125 -
libcpp/unittest/hdf/Makefile | 26 -
libcpp/unittest/normal.Makefile | 9 -
libcpp/unittest/normal.defines.mk | 54 -
libcpp/unittest/pbdata/CCSSequence_gtest.cpp | 117 -
libcpp/unittest/pbdata/ChangeListID_gtest.cpp | 34 -
libcpp/unittest/pbdata/DNASequence_gtest.cpp | 279 -
libcpp/unittest/pbdata/FASTAReader_gtest.cpp | 65 -
libcpp/unittest/pbdata/FASTASequence_gtest.cpp | 143 -
libcpp/unittest/pbdata/FASTQReader_gtest.cpp | 90 -
libcpp/unittest/pbdata/Makefile | 31 -
libcpp/unittest/pbdata/NucConversion_gtest.cpp | 105 -
libcpp/unittest/pbdata/SMRTSequence_gtest.cpp | 62 -
libcpp/unittest/pbdata/ScanData_gtest.cpp | 31 -
libcpp/unittest/pbdata/SeqUtils_gtest.cpp | 50 -
libcpp/unittest/pbdata/StringUtils_gtest.cpp | 80 -
libcpp/unittest/pbdata/VectorUtils_gtest.cpp | 38 -
libcpp/unittest/pbdata/defs_gtest.cpp | 44 -
.../pbdata/metagenome/TitleTable_gtest.cpp | 32 -
.../pbdata/qvs/QualityValueVector_gtest.cpp | 50 -
libcpp/unittest/pbdata/reads/ReadType_gtest.cpp | 57 -
libcpp/unittest/pbdata/saf/AlnGroup_gtest.cpp | 44 -
libcpp/unittest/pbdata/saf/MovieInfo_gtest.cpp | 43 -
libcpp/unittest/pbdata/saf/RefInfo_gtest.cpp | 45 -
libcpp/unittest/pbdata/testdata.h | 71 -
libcpp/unittest/pbdata/utils/SMRTTitle_gtest.cpp | 28 -
libcpp/unittest/pbdata/utils_gtest.cpp | 37 -
GNUmakefile => makefile | 35 +-
p4.common.mk | 147 -
p4.fetch.tmpmk | 10 -
p4.mk | 76 -
rules.mk | 16 +-
travis.sh | 2 +-
utils/.gitignore | 8 +
utils/Makefile | 64 -
utils/{GNUmakefile => makefile} | 28 +-
utils/p4.mk | 65 -
yli.common.mk | 94 -
yli.makefile | 80 -
506 files changed, 337 insertions(+), 96096 deletions(-)
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