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commit 2e5b367a193eb1c058382799c9f25cf6d867a556 Merge: 7a6ee9a fcd96a6 Author: Andreas Tille <[email protected]> Date: Mon Sep 15 14:58:26 2014 +0200 Merge tag 'upstream/1.5.2' Upstream version 1.5.2 .gitignore | 18 + .travis.yml | 8 + ABYSS/Abyss.cpp | 1 + ABYSS/Makefile.in | 590 -- AdjList/AdjList.cpp | 25 +- AdjList/Makefile.am | 1 - AdjList/Makefile.in | 591 -- Align/Makefile.in | 750 -- Align/align.cc | 2 +- Align/alignGlobal.h | 52 +- Align/mergepairs.cc | 10 +- Assembly/AssemblyAlgorithms.cpp | 39 +- Assembly/BranchRecord.cpp | 4 +- Assembly/ISequenceCollection.h | 7 +- Assembly/Makefile.in | 647 -- Assembly/Options.cpp | 37 +- Assembly/Options.h | 2 + Assembly/SequenceCollection.cpp | 73 +- Assembly/SequenceCollection.h | 1 + Bloom/Bloom.h | 324 + Bloom/BloomFilter.h | 100 + Bloom/BloomFilterWindow.h | 157 + Bloom/CascadingBloomFilter.h | 120 + Bloom/CascadingBloomFilterWindow.h | 90 + Bloom/ConcurrentBloomFilter.h | 96 + Bloom/Makefile.am | 20 + Bloom/bloom.cc | 571 ++ COPYRIGHT | 258 +- ChangeLog | 160 +- Common/Algorithms.h | 4 - Common/Alignment.h | 5 + Common/ConstString.h | 39 +- Common/Dictionary.h | 7 +- Common/Hash.h | 27 + Common/HashFunction.h | 5 + Common/Histogram.h | 21 +- Common/Kmer.cpp | 21 + Common/Kmer.h | 15 +- Common/KmerIterator.h | 110 + Common/Makefile.am | 5 + Common/Makefile.in | 775 -- Common/MemUtils.h | 18 + Common/SAM.h | 105 +- Common/StringUtil.h | 67 + Common/Uncompress.cpp | 1 + Common/UnorderedMap.h | 1 + Common/UnorderedSet.h | 21 + Common/Warnings.h | 6 + Common/cholesky.hpp | 4 - Consensus/Consensus.cpp | 2 +- Consensus/Makefile.in | 589 -- DAssembler/DAssembler.cpp | 2 +- DAssembler/Makefile.in | 618 -- DataLayer/FastaConcat.h | 89 + DataLayer/FastaReader.cpp | 33 +- DataLayer/FastaReader.h | 15 +- DataLayer/FastaWriter.cpp | 16 + DataLayer/FastaWriter.h | 6 + DataLayer/Makefile.am | 1 + DataLayer/Makefile.in | 706 -- DataLayer/Options.h | 1 + DataLayer/abyss-tofastq.cc | 2 +- DataLayer/fac.cc | 5 +- DistanceEst/DistanceEst.cpp | 55 +- DistanceEst/Makefile.am | 11 +- DistanceEst/Makefile.in | 615 -- FMIndex/FMIndex.h | 11 +- FMIndex/Makefile.in | 630 -- FMIndex/abyss-dawg.cc | 2 +- FMIndex/count.cc | 4 +- FMIndex/sais.hxx | 4 + FilterGraph/FilterGraph.cpp | 69 +- FilterGraph/Makefile.am | 1 - FilterGraph/Makefile.in | 593 -- GapFiller/Makefile.am | 17 + GapFiller/gapfill.cpp | 359 + GapFiller/gapfill.h | 70 + Graph/AllPathsSearch.h | 91 + Graph/Assemble.h | 5 +- Graph/BidirectionalBFS.h | 158 + Graph/BidirectionalBFSVisitor.h | 91 + Graph/BreadthFirstSearch.h | 72 + Graph/ConstrainedBFSVisitor.h | 158 + Graph/ConstrainedBidiBFSVisitor.h | 455 ++ Graph/ConstrainedSearch.cpp | 131 - Graph/ConstrainedSearch.h | 127 +- Graph/ContigGraphAlgorithms.h | 47 +- Graph/DefaultColorMap.h | 56 + Graph/DepthFirstSearch.h | 10 +- Graph/DotIO.h | 12 +- Graph/GraphAlgorithms.h | 48 + Graph/GraphIO.h | 2 + Graph/HashGraph.h | 485 ++ Graph/Makefile.am | 26 +- Graph/Makefile.in | 697 -- Graph/Path.h | 47 + Graph/PopBubbles.h | 1 - Graph/SAMIO.h | 33 +- Graph/gc.cc | 2 +- Graph/todot.cc | 2 +- KAligner/Aligner.h | 9 +- KAligner/KAligner.cpp | 4 +- KAligner/Makefile.am | 7 +- KAligner/Makefile.in | 620 -- Konnector/DBGBloom.h | 434 ++ Konnector/DBGBloomAlgorithms.h | 201 + Konnector/Makefile.am | 17 + Konnector/konnector.cc | 738 ++ Konnector/konnector.h | 341 + LICENSE | 872 ++- Layout/Makefile.in | 580 -- Layout/layout.cc | 9 +- LogKmerCount/CountingBloomFilter.h | 132 + LogKmerCount/Makefile.am | 16 + LogKmerCount/logcounter.cc | 164 + LogKmerCount/plc.h | 68 + LogKmerCount/plc_strand.h | 80 + Makefile.am | 16 +- Makefile.in | 856 --- Map/Makefile.am | 11 +- Map/Makefile.in | 669 -- Map/index.cc | 2 +- Map/map.cc | 188 +- Map/overlap.cc | 34 +- MergePaths/Makefile.am | 5 +- MergePaths/Makefile.in | 676 -- MergePaths/MergeContigs.cpp | 4 +- MergePaths/MergePaths.cpp | 4 +- MergePaths/PathConsensus.cpp | 16 +- Misc/Makefile.am | 2 +- Misc/Makefile.in | 538 -- Overlap/Makefile.am | 1 - Overlap/Makefile.in | 591 -- Overlap/Overlap.cpp | 29 +- Parallel/Makefile.in | 673 -- Parallel/NetworkSequenceCollection.cpp | 5 +- Parallel/parallelAbyss.cpp | 61 +- ParseAligns/Makefile.am | 9 +- ParseAligns/Makefile.in | 629 -- ParseAligns/ParseAligns.cpp | 4 +- ParseAligns/abyss-fixmate.cc | 53 +- PathOverlap/Makefile.am | 1 - PathOverlap/Makefile.in | 591 -- PathOverlap/PathOverlap.cpp | 25 +- PopBubbles/Makefile.am | 1 - PopBubbles/Makefile.in | 597 -- PopBubbles/PopBubbles.cpp | 99 +- README.html | 385 - README.md | 121 +- Scaffold/Makefile.am | 12 +- Scaffold/Makefile.in | 651 -- Scaffold/drawgraph.cc | 3 +- Scaffold/junction.cc | 8 +- Scaffold/longseqdist.cpp | 211 + Scaffold/scaffold.cc | 35 +- SimpleGraph/Makefile.am | 10 +- SimpleGraph/Makefile.in | 590 -- SimpleGraph/SimpleGraph.cpp | 7 +- Unittest/Common/BitUtilTest.cpp | 17 + Unittest/Common/HistogramTest.cpp | 53 + Unittest/Common/KmerIteratorTest.cpp | 48 + Unittest/Common/KmerTest.cpp | 32 + Unittest/Common/SAM.cc | 64 + Unittest/Common/Sequence.cc | 13 + Unittest/Common/StringUtilTest.cpp | 164 + Unittest/Graph/AllPathsSearchTest.cpp | 190 + Unittest/Graph/BidirectionalBFSTest.cpp | 185 + Unittest/Graph/ConstrainedBFSVisitorTest.cpp | 153 + Unittest/Graph/ConstrainedBidiBFSVisitorTest.cpp | 215 + Unittest/Graph/HashGraphTest.cpp | 87 + Unittest/Konnector/BloomFilter.cc | 323 + Unittest/Konnector/DBGBloomAlgorithmsTest.cpp | 173 + Unittest/Konnector/DBGBloomTest.cpp | 63 + Unittest/Konnector/integration-tests.mk | 370 + Unittest/Konnector/konnectorTest.cpp | 75 + Unittest/Makefile.am | 109 + aclocal.m4 | 1149 --- autogen.sh | 6 + bin/Makefile.am | 5 +- bin/Makefile.in | 478 -- bin/abyss-bloom-dist.mk | 187 + bin/abyss-bwamem | 78 + bin/abyss-joindist | 2 +- bin/abyss-pe | 184 +- bin/abyss-samtoafg | 1 + bin/abyss-tabtomd | 12 + compile | 347 - config.h.in | 285 - configure | 8868 ---------------------- configure.ac | 80 +- depcomp | 791 -- dialign/Makefile.in | 559 -- doc/ABYSS.1 | 7 +- doc/Makefile.am | 2 +- doc/Makefile.in | 499 -- doc/abyss-pe.1 | 57 +- doc/abyss-tofastq.1 | 4 +- doc/flowchart.graffle | 8498 +++++++++++++++++++++ doc/flowchart.pdf | Bin 165274 -> 165267 bytes doc/flowchart_simplified.graffle | 1806 +++++ doc/flowchart_simplified.pdf | Bin 0 -> 40801 bytes install-sh | 527 -- kmerprint/Makefile.am | 4 +- kmerprint/Makefile.in | 543 -- kmerprint/kmerprint.cc | 2 +- missing | 215 - 206 files changed, 21668 insertions(+), 31870 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/abyss.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
