[med-svn] [sga] branch debian updated (3eda594 -> 359711f)
Andreas Tille
tille at debian.org
Wed May 28 12:48:39 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian
in repository sga.
from 3eda594 Move debian/upstream to debian/upstream/metadata
adds b4efb32 Added namespace to fix compile error on OSX
adds f89c103 ld_set is static inline. Closes #29
adds dfe7463 Merge pull request #30 from sjackman/patch-1
adds 3cae268 Imported Upstream version 0.10.13
new 74057bd Merge tag 'upstream/0.10.13' into debian
new 631151a Upgrade to latest upstream version
new 5a78d5d cme fix dpkg-control
new 33a7871 Moved debian/upstream to debian/upstream/metadata
new a13af1b Move help2man call to override_dh_installman
new a532e5e Update patches to new upstream version
new ef3280c Remove Google addsense
new 38ef8cc Properly install manpages
new a4d0d49 Add README.Debian about sga-align and why examples can not (yet) be runned
new 359711f Merge branch 'debian' of git+ssh://git.debian.org/git/debian-med/sga into debian
The 10 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 +-
debian/README.Debian | 13 +
debian/changelog | 4 +-
debian/control | 22 +-
debian/manpages | 3 -
debian/patches/0002-no-rpath.patch | 27 +-
debian/patches/0003-do-not-dist-unsup-script.patch | 6 +-
.../patches/0004-Add-help-to-sga-bam2de.pl.patch | 12 +-
...0005-Remove-extensions-on-scripts-we-ship.patch | 6 +-
debian/patches/0006-remove-google-addsense.patch | 21 +
debian/patches/series | 3 +-
debian/rules | 33 +-
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 +
...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/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 +
176 files changed, 3042655 insertions(+), 8055 deletions(-)
create mode 100644 debian/README.Debian
delete mode 100644 debian/manpages
create mode 100644 debian/patches/0006-remove-google-addsense.patch
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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