[med-svn] [sga] branch master updated (dfe7463 -> 3cae268)
Andreas Tille
tille at debian.org
Wed May 28 12:32:00 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sga.
from dfe7463 Merge pull request #30 from sjackman/patch-1
new 3cae268 Imported Upstream version 0.10.13
The 1 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:
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 | 1625 +-
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 +
...eBuilder.h => PairedDeBruijnHaplotypeBuilder.h} | 23 +-
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-long.h | 26 -
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/{filter.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/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, 3042565 insertions(+), 7991 deletions(-)
delete mode 100644 src/Algorithm/HapgenProcess.cpp
delete mode 100644 src/Algorithm/HapgenProcess.h
delete mode 100644 src/Algorithm/LRCorrectionAlgorithm.cpp
delete mode 100644 src/Algorithm/LRCorrectionAlgorithm.h
delete mode 100644 src/Algorithm/LRCorrectionProcess.cpp
delete mode 100644 src/Algorithm/LRCorrectionProcess.h
delete mode 100644 src/Algorithm/MetAssembleProcess.cpp
delete mode 100644 src/Algorithm/MetAssembleProcess.h
delete mode 100644 src/Algorithm/MetagenomeBuilder.cpp
delete mode 100644 src/Algorithm/MetagenomeBuilder.h
delete mode 100644 src/Bigraph/TransitiveGroup.cpp
delete mode 100644 src/Bigraph/TransitiveGroup.h
delete mode 100644 src/Bigraph/TransitiveGroupCollection.cpp
delete mode 100644 src/Bigraph/TransitiveGroupCollection.h
create mode 100644 src/GraphDiff/DBGPathGuide.cpp
create mode 100644 src/GraphDiff/DBGPathGuide.h
create mode 100644 src/GraphDiff/IOverlapExtractor.h
create mode 100644 src/GraphDiff/OverlapExtractorWithCorrection.cpp
create mode 100644 src/GraphDiff/OverlapExtractorWithCorrection.h
create mode 100644 src/GraphDiff/PairedDeBruijnHaplotypeBuilder.cpp
copy src/GraphDiff/{DeBruijnHaplotypeBuilder.h => PairedDeBruijnHaplotypeBuilder.h} (59%)
create mode 100644 src/GraphDiff/StringHaplotypeBuilder.cpp
create mode 100644 src/GraphDiff/StringHaplotypeBuilder.h
delete mode 100644 src/SGA/convert-beetl.cpp
delete mode 100644 src/SGA/convert-beetl.h
delete mode 100644 src/SGA/correct-long.cpp
delete mode 100644 src/SGA/correct-long.h
delete mode 100644 src/SGA/hapgen.cpp
delete mode 100644 src/SGA/hapgen.h
create mode 100644 src/SGA/haplotype-filter.cpp
create mode 100644 src/SGA/haplotype-filter.h
delete mode 100644 src/SGA/metagenome.cpp
delete mode 100644 src/SGA/metagenome.h
create mode 100644 src/SGA/preqc.cpp
copy src/SGA/{filter.h => preqc.h} (58%)
create mode 100644 src/SGA/rewrite-evidence-bam.cpp
create mode 100644 src/SGA/rewrite-evidence-bam.h
delete mode 100644 src/SGA/var2vcf.cpp
delete mode 100644 src/SGA/var2vcf.h
delete mode 100644 src/StringGraph/SGDebugAlgorithms.cpp
delete mode 100644 src/StringGraph/SGDebugAlgorithms.h
delete mode 100644 src/StringGraph/SGPairedAlgorithms.cpp
delete mode 100644 src/StringGraph/SGPairedAlgorithms.h
delete mode 100644 src/SuffixTools/AssembleExact.cpp
delete mode 100644 src/SuffixTools/AssembleExact.h
delete mode 100644 src/Tests/Makefile.am
delete mode 100644 src/Tests/Tests.cpp
create mode 100644 src/Thirdparty/MurmurHash3.cpp
create mode 100644 src/Thirdparty/MurmurHash3.h
create mode 100644 src/Thirdparty/count_min_sketch.cpp
create mode 100644 src/Thirdparty/count_min_sketch.h
create mode 100644 src/Thirdparty/rapidjson/allocators.h
create mode 100644 src/Thirdparty/rapidjson/document.h
create mode 100644 src/Thirdparty/rapidjson/encodedstream.h
create mode 100644 src/Thirdparty/rapidjson/encodings.h
create mode 100644 src/Thirdparty/rapidjson/filereadstream.h
create mode 100644 src/Thirdparty/rapidjson/filestream.h
create mode 100644 src/Thirdparty/rapidjson/filewritestream.h
create mode 100644 src/Thirdparty/rapidjson/internal/pow10.h
create mode 100644 src/Thirdparty/rapidjson/internal/stack.h
create mode 100644 src/Thirdparty/rapidjson/internal/strfunc.h
create mode 100644 src/Thirdparty/rapidjson/prettywriter.h
create mode 100644 src/Thirdparty/rapidjson/rapidjson.h
create mode 100644 src/Thirdparty/rapidjson/rapidjson.license
create mode 100644 src/Thirdparty/rapidjson/reader.h
create mode 100644 src/Thirdparty/rapidjson/stringbuffer.h
create mode 100644 src/Thirdparty/rapidjson/writer.h
create mode 100644 src/Util/BloomFilter.cpp
create mode 100644 src/Util/BloomFilter.h
delete mode 100644 src/Util/ContigGraph.cpp
delete mode 100644 src/Util/ContigGraph.h
create mode 100644 src/Util/SGAStats.cpp
create mode 100644 src/Util/SGAStats.h
delete mode 100644 src/Util/SeqDAVG.cpp
delete mode 100644 src/Util/SeqDAVG.h
delete mode 100644 src/Util/SeqTrie.cpp
delete mode 100644 src/Util/SeqTrie.h
delete mode 100644 src/Util/Stats.cpp
delete mode 100644 src/Util/Stats.h
create mode 100644 src/Util/Verbosity.h
create mode 100755 src/bin/sga-call-variants.pl
create mode 100755 src/bin/sga-preqc-report.py
create mode 100755 src/bin/sga-variant-filters.pl
create mode 100755 src/bin/sga-vcf-dedup.pl
create mode 100644 src/examples/preqc/bird.preqc
create mode 100644 src/examples/preqc/fish.preqc
create mode 100644 src/examples/preqc/human.preqc
create mode 100644 src/examples/preqc/oyster.preqc
create mode 100644 src/examples/preqc/snake.preqc
create mode 100644 src/examples/preqc/yeast.preqc
create mode 100644 src/m4/m4_ax_openmp.m4
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