[med-svn] [abyss] 02/08: Merge tag 'upstream/1.5.2'
Andreas Tille
tille at debian.org
Mon Sep 15 14:27:22 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository abyss.
commit 2e5b367a193eb1c058382799c9f25cf6d867a556
Merge: 7a6ee9a fcd96a6
Author: Andreas Tille <tille at debian.org>
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(-)
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