[med-svn] [sga] 01/10: Merge tag 'upstream/0.10.13' into debian
Andreas Tille
tille at debian.org
Wed May 28 12:48:41 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian
in repository sga.
commit 74057bdc9c52a94a959837517ef5a83baaba0481
Merge: 96c51c6 3cae268
Author: Andreas Tille <tille at debian.org>
Date: Wed May 28 07:39:14 2014 +0200
Merge tag 'upstream/0.10.13' into debian
Upstream version 0.10.13
README.md | 2 +-
src/.gitignore | 3 +
src/Algorithm/ClusterProcess.cpp | 4 +
src/Algorithm/DPAlignment.h | 7 +-
src/Algorithm/ErrorCorrectProcess.cpp | 2 +-
src/Algorithm/HapgenProcess.cpp | 195 -
src/Algorithm/HapgenProcess.h | 102 -
src/Algorithm/KmerOverlaps.cpp | 281 +-
src/Algorithm/KmerOverlaps.h | 10 +
src/Algorithm/LRCorrectionAlgorithm.cpp | 248 -
src/Algorithm/LRCorrectionAlgorithm.h | 54 -
src/Algorithm/LRCorrectionProcess.cpp | 72 -
src/Algorithm/LRCorrectionProcess.h | 74 -
src/Algorithm/Makefile.am | 5 -
src/Algorithm/MetAssembleProcess.cpp | 224 -
src/Algorithm/MetAssembleProcess.h | 105 -
src/Algorithm/MetagenomeBuilder.cpp | 153 -
src/Algorithm/MetagenomeBuilder.h | 67 -
src/Algorithm/OverlapAlgorithm.cpp | 1 -
src/Algorithm/ReadCluster.cpp | 3 +-
src/Algorithm/StatsProcess.cpp | 15 +-
src/Algorithm/VariationBuilderCommon.h | 2 +-
src/Bigraph/Makefile.am | 2 -
src/Bigraph/TransitiveGroup.cpp | 91 -
src/Bigraph/TransitiveGroup.h | 48 -
src/Bigraph/TransitiveGroupCollection.cpp | 62 -
src/Bigraph/TransitiveGroupCollection.h | 41 -
src/Bigraph/Vertex.cpp | 164 -
src/Bigraph/Vertex.h | 12 +-
src/Concurrency/SequenceProcessFramework.h | 155 +-
src/GraphDiff/DBGPathGuide.cpp | 42 +
src/GraphDiff/DBGPathGuide.h | 38 +
src/GraphDiff/DeBruijnHaplotypeBuilder.cpp | 4 +-
src/GraphDiff/DindelRealignWindow.cpp | 1627 +-
src/GraphDiff/DindelRealignWindow.h | 196 +-
src/GraphDiff/DindelUtil.cpp | 79 +-
src/GraphDiff/DindelUtil.h | 11 +-
src/GraphDiff/GraphCompare.cpp | 340 +-
src/GraphDiff/GraphCompare.h | 59 +-
src/GraphDiff/HapgenUtil.cpp | 90 +-
src/GraphDiff/HapgenUtil.h | 7 +
src/GraphDiff/IOverlapExtractor.h | 27 +
src/GraphDiff/Makefile.am | 7 +-
src/GraphDiff/OverlapExtractorWithCorrection.cpp | 248 +
src/GraphDiff/OverlapExtractorWithCorrection.h | 78 +
src/GraphDiff/OverlapHaplotypeBuilder.cpp | 6 +-
src/GraphDiff/PairedDeBruijnHaplotypeBuilder.cpp | 247 +
src/GraphDiff/PairedDeBruijnHaplotypeBuilder.h | 58 +
src/GraphDiff/StringHaplotypeBuilder.cpp | 482 +
src/GraphDiff/StringHaplotypeBuilder.h | 94 +
src/GraphDiff/VCFTester.cpp | 3 +-
src/README | 18 +-
src/SGA/Makefile.am | 8 +-
src/SGA/assemble.cpp | 23 +-
src/SGA/cluster.cpp | 8 +-
src/SGA/convert-beetl.cpp | 165 -
src/SGA/convert-beetl.h | 18 -
src/SGA/correct-long.cpp | 246 -
src/SGA/correct.cpp | 2 +-
src/SGA/fm-merge.cpp | 12 +-
src/SGA/gapfill.cpp | 8 +-
src/SGA/graph-diff.cpp | 241 +-
src/SGA/hapgen.cpp | 233 -
src/SGA/hapgen.h | 23 -
src/SGA/haplotype-filter.cpp | 1118 +
src/SGA/haplotype-filter.h | 23 +
src/SGA/metagenome.cpp | 215 -
src/SGA/metagenome.h | 22 -
src/SGA/preprocess.cpp | 3 +-
src/SGA/preqc.cpp | 2123 +
src/SGA/{correct-long.h => preqc.h} | 13 +-
src/SGA/rewrite-evidence-bam.cpp | 208 +
src/SGA/rewrite-evidence-bam.h | 23 +
src/SGA/scaffold2fasta.cpp | 3 +-
src/SGA/sga.cpp | 76 +-
src/SGA/stats.cpp | 9 +-
src/SGA/subgraph.cpp | 2 -
src/SGA/var2vcf.cpp | 457 -
src/SGA/var2vcf.h | 28 -
src/SGA/walk.cpp | 2 -
src/Scaffold/ScaffoldSequenceCollection.cpp | 8 +-
src/StringGraph/Makefile.am | 2 -
src/StringGraph/SGAlgorithms.cpp | 107 +-
src/StringGraph/SGAlgorithms.h | 42 +-
src/StringGraph/SGDebugAlgorithms.cpp | 346 -
src/StringGraph/SGDebugAlgorithms.h | 70 -
src/StringGraph/SGPairedAlgorithms.cpp | 356 -
src/StringGraph/SGPairedAlgorithms.h | 85 -
src/StringGraph/SGSearch.cpp | 33 +-
src/StringGraph/SGVisitors.cpp | 673 +-
src/StringGraph/SGVisitors.h | 115 +-
src/SuffixTools/AssembleExact.cpp | 538 -
src/SuffixTools/AssembleExact.h | 80 -
src/SuffixTools/BWTAlgorithms.cpp | 109 +-
src/SuffixTools/BWTAlgorithms.h | 31 +-
src/SuffixTools/BWTIntervalCache.h | 4 +-
src/SuffixTools/PopulationIndex.cpp | 26 +-
src/SuffixTools/PopulationIndex.h | 11 +-
src/Tests/Makefile.am | 16 -
src/Tests/Tests.cpp | 130 -
src/Thirdparty/Makefile.am | 19 +-
src/Thirdparty/MurmurHash3.cpp | 335 +
src/Thirdparty/MurmurHash3.h | 37 +
src/Thirdparty/bcr.c | 2 +-
src/Thirdparty/count_min_sketch.cpp | 99 +
src/Thirdparty/count_min_sketch.h | 86 +
src/Thirdparty/multiple_alignment.cpp | 328 +-
src/Thirdparty/multiple_alignment.h | 75 +-
src/Thirdparty/overlapper.cpp | 321 +-
src/Thirdparty/overlapper.h | 24 +-
src/Thirdparty/rapidjson/allocators.h | 221 +
src/Thirdparty/rapidjson/document.h | 843 +
src/Thirdparty/rapidjson/encodedstream.h | 250 +
src/Thirdparty/rapidjson/encodings.h | 527 +
src/Thirdparty/rapidjson/filereadstream.h | 74 +
src/Thirdparty/rapidjson/filestream.h | 49 +
src/Thirdparty/rapidjson/filewritestream.h | 73 +
src/Thirdparty/rapidjson/internal/pow10.h | 54 +
src/Thirdparty/rapidjson/internal/stack.h | 83 +
src/Thirdparty/rapidjson/internal/strfunc.h | 24 +
src/Thirdparty/rapidjson/prettywriter.h | 160 +
src/Thirdparty/rapidjson/rapidjson.h | 256 +
src/Thirdparty/rapidjson/rapidjson.license | 19 +
src/Thirdparty/rapidjson/reader.h | 669 +
src/Thirdparty/rapidjson/stringbuffer.h | 50 +
src/Thirdparty/rapidjson/writer.h | 249 +
src/Util/Alphabet.h | 4 +-
src/Util/BitVector.h | 2 +-
src/Util/BloomFilter.cpp | 103 +
src/Util/BloomFilter.h | 73 +
src/Util/ContigGraph.cpp | 41 -
src/Util/ContigGraph.h | 25 -
src/Util/KmerDistribution.cpp | 67 +-
src/Util/KmerDistribution.h | 15 +-
src/Util/Makefile.am | 6 +-
src/Util/MultiAlignment.cpp | 19 +-
src/Util/MultiAlignment.h | 3 +
src/Util/MultiOverlap.h | 1 -
src/Util/Profiler.h | 3 +-
src/Util/SGAStats.cpp | 84 +
src/Util/SGAStats.h | 35 +
src/Util/SeqDAVG.cpp | 214 -
src/Util/SeqDAVG.h | 78 -
src/Util/SeqTrie.cpp | 331 -
src/Util/SeqTrie.h | 147 -
src/Util/Stats.cpp | 25 -
src/Util/Stats.h | 23 -
src/Util/StdAlnTools.cpp | 73 +-
src/Util/StdAlnTools.h | 19 +-
src/Util/VCFUtil.cpp | 2 -
src/Util/Verbosity.h | 35 +
src/bin/sga-call-variants.pl | 264 +
src/bin/sga-preqc-report.py | 860 +
src/bin/sga-variant-filters.pl | 115 +
src/bin/sga-vcf-dedup.pl | 22 +
src/configure.ac | 54 +-
src/examples/preqc/bird.preqc | 545303 +++++++++++++++++++
src/examples/preqc/fish.preqc | 509823 ++++++++++++++++++
src/examples/preqc/human.preqc | 562932 +++++++++++++++++++
src/examples/preqc/oyster.preqc | 511122 ++++++++++++++++++
src/examples/preqc/snake.preqc | 567867 ++++++++++++++++++++
src/examples/preqc/yeast.preqc | 331674 ++++++++++++
src/examples/sga-ecoli-miseq.sh | 10 +-
src/m4/m4_ax_openmp.m4 | 109 +
164 files changed, 3042610 insertions(+), 7959 deletions(-)
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