[med-svn] [abyss] branch master updated (03a15c6 -> 23461e6)
Andreas Tille
tille at debian.org
Thu Jul 16 09:42:31 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository abyss.
from 03a15c6 cme fix dpkg-control and upload to unstable
new ca88ee1 Imported Upstream version 1.9.0
new a01c105 Merge tag 'upstream/1.9.0'
new bad2199 New upstream version
new c8fcee6 Take over COPYRIGHT from upstream that was heavily adapted
new a94c490 Dropped Shaun Jackman from Uploaders since he confirmed that he will not be able to maintain the package
new df777c9 add debian/* paragraph
new 852531c Adapted patches (including deactivating gtest patch since it needs severe changes
new f25d4fe Build-Depends: libsqlite3-dev
new 8210a6c Script uses bash syntax so request bash interpreter
new 23461e6 Upload to unstable
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:
.travis.yml | 10 +-
ABYSS/Makefile.am | 9 +-
ABYSS/{Abyss.cpp => abyss.cc} | 58 +-
AdjList/AdjList.cpp | 229 +-
AdjList/Makefile.am | 13 +
Align/mergepairs.cc | 4 +-
Assembly/AdjacencyAlgorithm.h | 50 +
Assembly/AssembleAlgorithm.h | 146 +
Assembly/AssemblyAlgorithms.cc | 20 +
Assembly/AssemblyAlgorithms.cpp | 1049 ----
Assembly/AssemblyAlgorithms.h | 214 +-
Assembly/BranchGroup.cpp | 86 -
Assembly/BranchGroup.h | 105 +-
Assembly/BranchRecord.cpp | 59 -
Assembly/BranchRecord.h | 149 +-
Assembly/{BranchRecord.h => BranchRecordBase.h} | 65 +-
Assembly/BubbleAlgorithm.h | 279 ++
Assembly/CoverageAlgorithm.h | 117 +
Assembly/DBG.h | 913 ++++
Assembly/DotWriter.cpp | 70 -
Assembly/DotWriter.h | 217 +-
Assembly/ErodeAlgorithm.h | 117 +
Assembly/ISequenceCollection.h | 88 -
Assembly/LoadAlgorithm.h | 182 +
Assembly/Makefile.am | 32 +-
Assembly/{Options.cpp => Options.cc} | 82 +-
Assembly/Options.h | 8 +
{Common => Assembly}/SeqExt.h | 36 +-
Assembly/SequenceCollection.cpp | 291 --
Assembly/SequenceCollection.h | 353 +-
Assembly/SplitAlgorithm.h | 97 +
Assembly/TrimAlgorithm.h | 203 +
Assembly/{KmerData.h => VertexData.h} | 75 +-
Bloom/Bloom.h | 162 +-
Bloom/BloomFilter.h | 89 +-
Bloom/BloomFilterWindow.h | 42 +-
Bloom/CascadingBloomFilter.h | 16 +-
Bloom/CascadingBloomFilterWindow.h | 11 +-
Bloom/bloom.cc | 58 +-
CITATION.bib | 10 +
CITATION.md | 39 +
ChangeLog | 42 +
Common/BitUtil.h | 107 +
Common/ContigProperties.h | 6 +-
Common/Estimate.h | 7 +
Common/Histogram.h | 44 +-
Common/InsOrderedMap.h | 88 +
Common/Kmer.cpp | 10 +-
Common/Kmer.h | 25 +-
Common/KmerSet.h | 47 +
Common/Makefile.am | 5 +-
Common/MemUtils.h | 4 +-
Common/SAM.h | 3 +-
Common/SeqExt.cpp | 16 -
Common/Sequence.cpp | 4 +-
Common/Sequence.h | 82 +
Common/StringUtil.h | 78 +-
Common/VectorUtil.h | 35 +
Common/Warnings.h | 6 -
DataBase/DB.cc | 208 +
DataBase/DB.h | 227 +
DataBase/Makefile.am | 11 +
DataBase/Options.h | 22 +
DataBase/abyss-db-txt | 35 +
DataBase/db-csv.cc | 124 +
DataLayer/FastaReader.cpp | 4 +-
DataLayer/FastaReader.h | 4 +-
DataLayer/FastaWriter.h | 2 +-
DataLayer/Makefile.am | 9 +-
DataLayer/abyss-tofastq.cc | 8 +-
DataLayer/fac.cc | 6 +-
DistanceEst/DistanceEst.cpp | 111 +-
DistanceEst/MLE.cpp | 64 +-
DistanceEst/Makefile.am | 2 +
FilterGraph/{FilterGraph.cpp => FilterGraph.cc} | 286 +-
FilterGraph/Makefile.am | 2 +-
Graph/AllPathsSearch.h | 1 -
Graph/AsqgIO.h | 24 +-
Graph/BidirectionalBFSVisitor.h | 48 +-
Graph/ConstrainedBidiBFSVisitor.h | 14 +-
Graph/ConstrainedSearch.h | 8 +-
Graph/ContigGraph.h | 2 +-
Graph/ContigGraphAlgorithms.h | 14 +-
Graph/DirectedGraph.h | 9 +-
Graph/ExtendPath.h | 296 ++
Graph/{AsqgIO.h => GfaIO.h} | 118 +-
Graph/GraphAlgorithms.h | 25 +-
Graph/GraphIO.h | 21 +-
Graph/GraphUtil.h | 52 +-
Graph/HashGraph.h | 24 +-
Graph/Makefile.am | 2 +
Graph/Options.h | 2 +-
Graph/Path.h | 6 +-
Graph/SAMIO.h | 2 +-
Graph/todot.cc | 19 +-
IntegrationTest/DIDA/alignment-test.mk | 84 +
IntegrationTest/DIDA/assembly-test.mk | 83 +
IntegrationTest/DIDA/compare-fastx | 14 +
IntegrationTest/DIDA/compare-sam | 110 +
Konnector/DBGBloom.h | 4 +-
Konnector/DBGBloomAlgorithms.h | 122 +-
Konnector/konnector.cc | 683 ++-
Konnector/konnector.h | 485 +-
LogKmerCount/logcounter.cc | 4 +-
Makefile.am | 31 +-
Map/Makefile.am | 4 +-
Map/index.cc | 18 +-
Map/map.cc | 109 +-
Map/overlap.cc | 4 +-
MergePaths/Makefile.am | 6 +
MergePaths/MergeContigs.cpp | 84 +-
MergePaths/MergePaths.cpp | 74 +-
MergePaths/PathConsensus.cpp | 77 +-
Overlap/Overlap.cpp | 15 +-
PairedDBG/BranchRecord.h | 43 +
PairedDBG/Dinuc.h | 167 +
PairedDBG/KmerPair.cc | 4 +
PairedDBG/KmerPair.h | 229 +
PairedDBG/Makefile.am | 26 +
PairedDBG/PairedDBGAlgorithms.h | 42 +
PairedDBG/SequenceCollection.h | 24 +
PairedDBG/abyss-paired-dbg.cc | 1 +
Parallel/CommLayer.cpp | 4 +-
Parallel/Makefile.am | 20 +-
Parallel/MessageBuffer.cpp | 16 +-
Parallel/MessageBuffer.h | 22 +-
Parallel/Messages.h | 45 +-
Parallel/NetworkSequenceCollection.cpp | 171 +-
Parallel/NetworkSequenceCollection.h | 118 +-
Parallel/SequenceCollection.h | 10 +
Parallel/parallelAbyss.cpp | 37 +-
ParseAligns/Makefile.am | 2 +
ParseAligns/abyss-fixmate.cc | 98 +-
PathOverlap/Makefile.am | 2 +
PathOverlap/PathOverlap.cpp | 58 +-
PopBubbles/PopBubbles.cpp | 38 +-
README.md | 111 +-
Scaffold/Makefile.am | 2 +
Scaffold/drawgraph.cc | 89 +-
Scaffold/junction.cc | 2 +-
Scaffold/scaffold.cc | 152 +-
Sealer/Makefile.am | 29 +
Sealer/README.md | 171 +
Sealer/sealer.cc | 1025 ++++
SimpleGraph/Makefile.am | 2 +
SimpleGraph/SimpleGraph.cpp | 84 +-
Unittest/Common/BitUtilTest.cpp | 230 +
Unittest/Common/StringUtilTest.cpp | 30 +-
Unittest/DBG/LoadAlgorithmTest.cpp | 43 +
Unittest/Graph/AllPathsSearchTest.cpp | 1 -
Unittest/Graph/BidirectionalBFSTest.cpp | 31 +-
Unittest/Graph/ConstrainedBidiBFSVisitorTest.cpp | 1 -
Unittest/Graph/ExtendPathTest.cpp | 345 ++
Unittest/Konnector/BloomFilter.cc | 41 +-
Unittest/Konnector/DBGBloomAlgorithmsTest.cpp | 77 +-
Unittest/Konnector/DBGBloomTest.cpp | 2 +-
Unittest/Konnector/integration-tests.mk | 8 +-
Unittest/Makefile.am | 213 +-
Unittest/PairedDBG/BranchRecordTest.cpp | 58 +
Unittest/PairedDBG/DinucTest.cc | 82 +
Unittest/PairedDBG/KmerPairTest.cc | 96 +
Unittest/PairedDBG/LoadAlgorithmTest.cpp | 53 +
Unittest/PairedDBG/test.fa | 2 +
Unittest/PairedDBG/test.png | Bin 0 -> 156866 bytes
Unittest/PairedDBG/test.svg | 859 ++++
bin/Makefile.am | 14 +-
bin/abyss-dida | 107 +
bin/abyss-fac.pl | 4 +-
bin/abyss-fatoagp | 2 +
bin/abyss-nompi | 6 +
bin/abyss-pe | 254 +-
circle.yml | 11 +
configure.ac | 110 +-
debian/changelog | 12 +
debian/control | 6 +-
debian/copyright | 269 +-
debian/patches/abyss-32-bit.patch | 64 +-
debian/patches/{abyss-pe => abyss-pe.patch} | 3 +
debian/patches/fix_bash_script.patch | 12 +
debian/patches/gtest.patch | 2 +
debian/patches/privacy-breach.patch | 2 +-
debian/patches/series | 5 +-
doc/ABYSS.1 | 4 +-
doc/abyss-pe.1 | 55 +-
doc/abyss-tofastq.1 | 4 +-
doc/flowchart.graffle | 2 +-
lib/gtest-1.7.0/CHANGES | 157 +
lib/gtest-1.7.0/CONTRIBUTORS | 37 +
lib/gtest-1.7.0/LICENSE | 28 +
lib/gtest-1.7.0/Makefile.am | 42 +
lib/gtest-1.7.0/README | 435 ++
lib/gtest-1.7.0/include/gtest/gtest-death-test.h | 294 ++
lib/gtest-1.7.0/include/gtest/gtest-message.h | 250 +
lib/gtest-1.7.0/include/gtest/gtest-param-test.h | 1421 ++++++
.../include/gtest/gtest-param-test.h.pump | 487 ++
lib/gtest-1.7.0/include/gtest/gtest-printers.h | 855 ++++
lib/gtest-1.7.0/include/gtest/gtest-spi.h | 232 +
lib/gtest-1.7.0/include/gtest/gtest-test-part.h | 179 +
lib/gtest-1.7.0/include/gtest/gtest-typed-test.h | 259 +
lib/gtest-1.7.0/include/gtest/gtest.h | 2291 +++++++++
lib/gtest-1.7.0/include/gtest/gtest_pred_impl.h | 358 ++
lib/gtest-1.7.0/include/gtest/gtest_prod.h | 58 +
.../gtest/internal/gtest-death-test-internal.h | 319 ++
.../include/gtest/internal/gtest-filepath.h | 206 +
.../include/gtest/internal/gtest-internal.h | 1158 +++++
.../include/gtest/internal/gtest-linked_ptr.h | 233 +
.../gtest/internal/gtest-param-util-generated.h | 5143 ++++++++++++++++++++
.../internal/gtest-param-util-generated.h.pump | 301 ++
.../include/gtest/internal/gtest-param-util.h | 619 +++
.../include/gtest/internal/gtest-port.h | 1947 ++++++++
.../include/gtest/internal/gtest-string.h | 167 +
.../include/gtest/internal/gtest-tuple.h | 1012 ++++
.../include/gtest/internal/gtest-tuple.h.pump | 339 ++
.../include/gtest/internal/gtest-type-util.h | 3331 +++++++++++++
.../include/gtest/internal/gtest-type-util.h.pump | 297 ++
lib/gtest-1.7.0/src/gtest-all.cc | 48 +
lib/gtest-1.7.0/src/gtest-death-test.cc | 1344 +++++
lib/gtest-1.7.0/src/gtest-filepath.cc | 382 ++
lib/gtest-1.7.0/src/gtest-internal-inl.h | 1218 +++++
lib/gtest-1.7.0/src/gtest-port.cc | 805 +++
lib/gtest-1.7.0/src/gtest-printers.cc | 363 ++
lib/gtest-1.7.0/src/gtest-test-part.cc | 110 +
lib/gtest-1.7.0/src/gtest-typed-test.cc | 110 +
lib/gtest-1.7.0/src/gtest.cc | 5015 +++++++++++++++++++
lib/gtest-1.7.0/src/gtest_main.cc | 38 +
m4/m4_ax_pthread.m4 | 332 ++
226 files changed, 44526 insertions(+), 3943 deletions(-)
rename ABYSS/{Abyss.cpp => abyss.cc} (75%)
create mode 100644 Assembly/AdjacencyAlgorithm.h
create mode 100644 Assembly/AssembleAlgorithm.h
create mode 100644 Assembly/AssemblyAlgorithms.cc
delete mode 100644 Assembly/AssemblyAlgorithms.cpp
delete mode 100644 Assembly/BranchGroup.cpp
delete mode 100644 Assembly/BranchRecord.cpp
copy Assembly/{BranchRecord.h => BranchRecordBase.h} (65%)
create mode 100644 Assembly/BubbleAlgorithm.h
create mode 100644 Assembly/CoverageAlgorithm.h
create mode 100644 Assembly/DBG.h
delete mode 100644 Assembly/DotWriter.cpp
create mode 100644 Assembly/ErodeAlgorithm.h
delete mode 100644 Assembly/ISequenceCollection.h
create mode 100644 Assembly/LoadAlgorithm.h
rename Assembly/{Options.cpp => Options.cc} (80%)
rename {Common => Assembly}/SeqExt.h (64%)
delete mode 100644 Assembly/SequenceCollection.cpp
create mode 100644 Assembly/SplitAlgorithm.h
create mode 100644 Assembly/TrimAlgorithm.h
rename Assembly/{KmerData.h => VertexData.h} (69%)
create mode 100644 CITATION.bib
create mode 100644 CITATION.md
create mode 100644 Common/InsOrderedMap.h
create mode 100644 Common/KmerSet.h
delete mode 100644 Common/SeqExt.cpp
create mode 100644 Common/VectorUtil.h
delete mode 100644 Common/Warnings.h
create mode 100644 DataBase/DB.cc
create mode 100644 DataBase/DB.h
create mode 100644 DataBase/Makefile.am
create mode 100644 DataBase/Options.h
create mode 100755 DataBase/abyss-db-txt
create mode 100644 DataBase/db-csv.cc
rename FilterGraph/{FilterGraph.cpp => FilterGraph.cc} (65%)
create mode 100644 Graph/ExtendPath.h
copy Graph/{AsqgIO.h => GfaIO.h} (55%)
create mode 100755 IntegrationTest/DIDA/alignment-test.mk
create mode 100755 IntegrationTest/DIDA/assembly-test.mk
create mode 100755 IntegrationTest/DIDA/compare-fastx
create mode 100755 IntegrationTest/DIDA/compare-sam
create mode 100644 PairedDBG/BranchRecord.h
create mode 100644 PairedDBG/Dinuc.h
create mode 100644 PairedDBG/KmerPair.cc
create mode 100644 PairedDBG/KmerPair.h
create mode 100644 PairedDBG/Makefile.am
create mode 100644 PairedDBG/PairedDBGAlgorithms.h
create mode 100644 PairedDBG/SequenceCollection.h
create mode 100644 PairedDBG/abyss-paired-dbg.cc
create mode 100644 Parallel/SequenceCollection.h
create mode 100644 Sealer/Makefile.am
create mode 100644 Sealer/README.md
create mode 100644 Sealer/sealer.cc
create mode 100644 Unittest/DBG/LoadAlgorithmTest.cpp
create mode 100644 Unittest/Graph/ExtendPathTest.cpp
create mode 100644 Unittest/PairedDBG/BranchRecordTest.cpp
create mode 100644 Unittest/PairedDBG/DinucTest.cc
create mode 100644 Unittest/PairedDBG/KmerPairTest.cc
create mode 100644 Unittest/PairedDBG/LoadAlgorithmTest.cpp
create mode 100644 Unittest/PairedDBG/test.fa
create mode 100644 Unittest/PairedDBG/test.png
create mode 100644 Unittest/PairedDBG/test.svg
create mode 100755 bin/abyss-dida
create mode 100755 bin/abyss-nompi
create mode 100644 circle.yml
rename debian/patches/{abyss-pe => abyss-pe.patch} (74%)
create mode 100644 debian/patches/fix_bash_script.patch
create mode 100644 lib/gtest-1.7.0/CHANGES
create mode 100644 lib/gtest-1.7.0/CONTRIBUTORS
create mode 100644 lib/gtest-1.7.0/LICENSE
create mode 100644 lib/gtest-1.7.0/Makefile.am
create mode 100644 lib/gtest-1.7.0/README
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-death-test.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-message.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-param-test.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-param-test.h.pump
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-printers.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-spi.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-test-part.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest-typed-test.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest_pred_impl.h
create mode 100644 lib/gtest-1.7.0/include/gtest/gtest_prod.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-death-test-internal.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-filepath.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-internal.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-linked_ptr.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-param-util-generated.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-param-util-generated.h.pump
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-param-util.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-port.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-string.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-tuple.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-tuple.h.pump
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-type-util.h
create mode 100644 lib/gtest-1.7.0/include/gtest/internal/gtest-type-util.h.pump
create mode 100644 lib/gtest-1.7.0/src/gtest-all.cc
create mode 100644 lib/gtest-1.7.0/src/gtest-death-test.cc
create mode 100644 lib/gtest-1.7.0/src/gtest-filepath.cc
create mode 100644 lib/gtest-1.7.0/src/gtest-internal-inl.h
create mode 100644 lib/gtest-1.7.0/src/gtest-port.cc
create mode 100644 lib/gtest-1.7.0/src/gtest-printers.cc
create mode 100644 lib/gtest-1.7.0/src/gtest-test-part.cc
create mode 100644 lib/gtest-1.7.0/src/gtest-typed-test.cc
create mode 100644 lib/gtest-1.7.0/src/gtest.cc
create mode 100644 lib/gtest-1.7.0/src/gtest_main.cc
create mode 100644 m4/m4_ax_pthread.m4
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