[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


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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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