[med-svn] [abyss] branch master updated (7a6ee9a -> 438a8ff)
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 change to branch master
in repository abyss.
from 7a6ee9a New upstream version at github
new fcd96a6 Imported Upstream version 1.5.2
new 2e5b367 Merge tag 'upstream/1.5.2'
new 825341a Option --disable-popcnt vanished
new 060eeff Patch applied upstream
new 4afb922 Use dh-autoreconf
new 4196600 Build-Depends: libtext-multimarkdown-perl
new 49c2b34 cme fix dpkg-control
new 438a8ff libgtest-dev to enable unit tests at build time (does not work unfortunately)
The 8 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:
.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-bwasw => abyss-bwamem} | 24 +-
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 +-
debian/README.Debian | 24 -
debian/changelog | 6 +-
debian/control | 11 +-
debian/patches/abyss-pe | 10 +-
debian/patches/gcc4.8.patch | 32 -
debian/patches/series | 1 -
debian/rules | 4 +-
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 -
213 files changed, 21622 insertions(+), 31950 deletions(-)
create mode 100644 .gitignore
create mode 100644 .travis.yml
delete mode 100644 ABYSS/Makefile.in
delete mode 100644 AdjList/Makefile.in
delete mode 100644 Align/Makefile.in
delete mode 100644 Assembly/Makefile.in
create mode 100644 Bloom/Bloom.h
create mode 100644 Bloom/BloomFilter.h
create mode 100644 Bloom/BloomFilterWindow.h
create mode 100644 Bloom/CascadingBloomFilter.h
create mode 100644 Bloom/CascadingBloomFilterWindow.h
create mode 100644 Bloom/ConcurrentBloomFilter.h
create mode 100644 Bloom/Makefile.am
create mode 100644 Bloom/bloom.cc
create mode 100644 Common/Hash.h
create mode 100644 Common/KmerIterator.h
delete mode 100644 Common/Makefile.in
create mode 100644 Common/MemUtils.h
create mode 100644 Common/UnorderedSet.h
create mode 100644 Common/Warnings.h
delete mode 100644 Consensus/Makefile.in
delete mode 100644 DAssembler/Makefile.in
create mode 100644 DataLayer/FastaConcat.h
delete mode 100644 DataLayer/Makefile.in
delete mode 100644 DistanceEst/Makefile.in
delete mode 100644 FMIndex/Makefile.in
delete mode 100644 FilterGraph/Makefile.in
create mode 100644 GapFiller/Makefile.am
create mode 100644 GapFiller/gapfill.cpp
create mode 100644 GapFiller/gapfill.h
create mode 100644 Graph/AllPathsSearch.h
create mode 100644 Graph/BidirectionalBFS.h
create mode 100644 Graph/BidirectionalBFSVisitor.h
create mode 100644 Graph/BreadthFirstSearch.h
create mode 100644 Graph/ConstrainedBFSVisitor.h
create mode 100644 Graph/ConstrainedBidiBFSVisitor.h
delete mode 100644 Graph/ConstrainedSearch.cpp
create mode 100644 Graph/DefaultColorMap.h
create mode 100644 Graph/HashGraph.h
delete mode 100644 Graph/Makefile.in
create mode 100644 Graph/Path.h
delete mode 100644 KAligner/Makefile.in
create mode 100644 Konnector/DBGBloom.h
create mode 100644 Konnector/DBGBloomAlgorithms.h
create mode 100644 Konnector/Makefile.am
create mode 100644 Konnector/konnector.cc
create mode 100644 Konnector/konnector.h
delete mode 100644 Layout/Makefile.in
create mode 100644 LogKmerCount/CountingBloomFilter.h
create mode 100644 LogKmerCount/Makefile.am
create mode 100644 LogKmerCount/logcounter.cc
create mode 100644 LogKmerCount/plc.h
create mode 100644 LogKmerCount/plc_strand.h
delete mode 100644 Makefile.in
delete mode 100644 Map/Makefile.in
delete mode 100644 MergePaths/Makefile.in
delete mode 100644 Misc/Makefile.in
delete mode 100644 Overlap/Makefile.in
delete mode 100644 Parallel/Makefile.in
delete mode 100644 ParseAligns/Makefile.in
delete mode 100644 PathOverlap/Makefile.in
delete mode 100644 PopBubbles/Makefile.in
delete mode 100644 README.html
delete mode 100644 Scaffold/Makefile.in
create mode 100644 Scaffold/longseqdist.cpp
delete mode 100644 SimpleGraph/Makefile.in
create mode 100644 Unittest/Common/BitUtilTest.cpp
create mode 100644 Unittest/Common/HistogramTest.cpp
create mode 100644 Unittest/Common/KmerIteratorTest.cpp
create mode 100644 Unittest/Common/KmerTest.cpp
create mode 100644 Unittest/Common/SAM.cc
create mode 100644 Unittest/Common/Sequence.cc
create mode 100644 Unittest/Common/StringUtilTest.cpp
create mode 100644 Unittest/Graph/AllPathsSearchTest.cpp
create mode 100644 Unittest/Graph/BidirectionalBFSTest.cpp
create mode 100644 Unittest/Graph/ConstrainedBFSVisitorTest.cpp
create mode 100644 Unittest/Graph/ConstrainedBidiBFSVisitorTest.cpp
create mode 100644 Unittest/Graph/HashGraphTest.cpp
create mode 100644 Unittest/Konnector/BloomFilter.cc
create mode 100644 Unittest/Konnector/DBGBloomAlgorithmsTest.cpp
create mode 100644 Unittest/Konnector/DBGBloomTest.cpp
create mode 100755 Unittest/Konnector/integration-tests.mk
create mode 100644 Unittest/Konnector/konnectorTest.cpp
create mode 100644 Unittest/Makefile.am
delete mode 100644 aclocal.m4
create mode 100755 autogen.sh
delete mode 100644 bin/Makefile.in
create mode 100755 bin/abyss-bloom-dist.mk
copy bin/{abyss-bwasw => abyss-bwamem} (71%)
create mode 100755 bin/abyss-tabtomd
delete mode 100755 compile
delete mode 100644 config.h.in
delete mode 100755 configure
delete mode 100644 debian/README.Debian
delete mode 100755 depcomp
delete mode 100644 dialign/Makefile.in
delete mode 100644 doc/Makefile.in
create mode 100644 doc/flowchart.graffle
create mode 100644 doc/flowchart_simplified.graffle
create mode 100644 doc/flowchart_simplified.pdf
delete mode 100755 install-sh
delete mode 100644 kmerprint/Makefile.in
delete mode 100755 missing
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