[med-svn] [gatb-core] branch upstream updated (b8c3a15 -> 51eb9b0)
Andreas Tille
tille at debian.org
Fri Dec 1 14:31:39 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository gatb-core.
from b8c3a15 New upstream version 1.3.0+dfsg
new 51eb9b0 New upstream version 1.4.0+dfsg
The 1 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 | 31 +
README.md | 9 +-
gatb-core/.gitignore | 3 +
gatb-core/CMakeLists.txt | 15 +-
gatb-core/RELEASES.md | 84 +
gatb-core/cmake/Delivery.cmake | 2 +-
gatb-core/cmake/GetDate.cmake | 31 -
gatb-core/doc/doxygen/src/mainpage.hpp | 10 +-
gatb-core/doc/doxygen/src/snippetspage.hpp | 45 +-
gatb-core/docker/Dockerfile.clang | 5 +-
gatb-core/examples/.DS_Store | Bin 10244 -> 0 bytes
gatb-core/examples/Makefile | 24 +
gatb-core/examples/README.md | 94 +
gatb-core/examples/bank/bank15.cpp | 16 +-
gatb-core/examples/bank/bank21.cpp | 97 +
gatb-core/examples/bank/bank22.cpp | 50 +
gatb-core/examples/bank/{bank15.cpp => bank23.cpp} | 21 +-
gatb-core/examples/bank/bank24.cpp | 77 +
gatb-core/examples/bank/bank25.cpp | 93 +
gatb-core/examples/bank/{bank2.cpp => bank26.cpp} | 18 +-
gatb-core/examples/bank/{bank14.cpp => bank27.cpp} | 29 +-
gatb-core/examples/bank/{bank14.cpp => bank28.cpp} | 29 +-
gatb-core/examples/kmer/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/examples/storage/.DS_Store | Bin 6148 -> 0 bytes
.../{multithreading6.cpp => multithreading8.cpp} | 49 +-
gatb-core/scripts/NewProject/CMakeLists.txt | 6 +-
gatb-core/scripts/delivery_compile.sh | 2 +-
gatb-core/scripts/make_official_release.sh | 2 +-
gatb-core/src/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/src/gatb/.DS_Store | Bin 8196 -> 0 bytes
gatb-core/src/gatb/bank/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/src/gatb/bank/api/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/src/gatb/bank/api/Sequence.hpp | 116 +
gatb-core/src/gatb/bank/impl/AbstractBank.hpp | 2 +-
gatb-core/src/gatb/bank/impl/Bank.cpp | 18 +
gatb-core/src/gatb/bank/impl/BankBinary.cpp | 2 +-
gatb-core/src/gatb/bank/impl/BankFasta.cpp | 6 +-
gatb-core/src/gatb/bcalm2/bcalm_algo.cpp | 648 ++++--
gatb-core/src/gatb/bcalm2/bcalm_algo.hpp | 88 +-
gatb-core/src/gatb/bcalm2/bglue_algo.cpp | 922 ++++----
gatb-core/src/gatb/bcalm2/bglue_algo.hpp | 158 +-
gatb-core/src/gatb/bcalm2/lockstdqueue.h | 52 -
gatb-core/src/gatb/bcalm2/logging.cpp | 40 +
gatb-core/src/gatb/bcalm2/logging.hpp | 6 +
gatb-core/src/gatb/bcalm2/ograph.cpp | 340 ++-
gatb-core/src/gatb/bcalm2/ograph.h | 22 +-
gatb-core/src/gatb/debruijn/impl/ExtremityInfo.hpp | 4 +
gatb-core/src/gatb/debruijn/impl/Graph.cpp | 23 +-
gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp | 621 ++++-
gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp | 39 +-
.../src/gatb/debruijn/impl/IterativeExtensions.cpp | 24 +-
gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp | 381 +++
.../config.hpp.in => debruijn/impl/LinkTigs.hpp} | 30 +-
.../src/gatb/debruijn/impl/Simplifications.cpp | 220 +-
.../src/gatb/debruijn/impl/Simplifications.hpp | 15 +-
.../debruijn/impl/UnitigsConstructionAlgorithm.cpp | 194 +-
.../debruijn/impl/UnitigsConstructionAlgorithm.hpp | 29 +-
gatb-core/src/gatb/debruijn/impl/dag_vector.hpp | 325 +++
gatb-core/src/gatb/debruijn/impl/rank_vector.hpp | 137 ++
gatb-core/src/gatb/gatb_core.hpp | 5 +-
gatb-core/src/gatb/kmer/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/src/gatb/kmer/impl/.DS_Store | Bin 10244 -> 0 bytes
.../src/gatb/kmer/impl/ConfigurationAlgorithm.cpp | 4 +-
.../src/gatb/kmer/impl/CountProcessorHistogram.hpp | 3 +
gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp | 20 +-
gatb-core/src/gatb/kmer/impl/Model.hpp | 256 +-
gatb-core/src/gatb/kmer/impl/PartiInfo.hpp | 28 +-
gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp | 1477 ++++++++++--
gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp | 236 +-
.../src/gatb/kmer/impl/RepartitionAlgorithm.cpp | 10 +-
.../src/gatb/kmer/impl/Sequence2SuperKmer.hpp | 9 +
.../src/gatb/kmer/impl/SortingCountAlgorithm.cpp | 583 ++++-
.../src/gatb/kmer/impl/SortingCountAlgorithm.hpp | 6 +
gatb-core/src/gatb/system/api/Exception.hpp | 19 +-
gatb-core/src/gatb/system/impl/FileSystemLinux.cpp | 2 +-
gatb-core/src/gatb/system/impl/FileSystemMacos.cpp | 2 +-
.../src/gatb/system/impl/SystemInfoCommon.cpp | 1 -
gatb-core/src/gatb/system/impl/ThreadLinux.cpp | 15 +-
gatb-core/src/gatb/system/impl/ThreadMacos.cpp | 16 +-
.../gatb/template/TemplateSpecialization10.cpp.in | 8 +-
gatb-core/src/gatb/tools/.DS_Store | Bin 6148 -> 0 bytes
.../src/gatb/tools/collections/impl/Hash16.hpp | 5 +
.../gatb/tools/collections/impl/IteratorFile.hpp | 10 +-
.../src/gatb/tools/collections/impl/MapMPHF.hpp | 311 ++-
gatb-core/src/gatb/tools/compression/DnaCoder.cpp | 1784 ++++++++++++++
gatb-core/src/gatb/tools/compression/DnaCoder.hpp | 307 +++
.../src/gatb/tools/compression/HeaderCoder.cpp | 789 +++++++
.../src/gatb/tools/compression/HeaderCoder.hpp | 186 ++
gatb-core/src/gatb/tools/compression/Leon.cpp | 2434 ++++++++++++++++++++
gatb-core/src/gatb/tools/compression/Leon.hpp | 490 ++++
.../src/gatb/tools/compression/RangeCoder.cpp | 2 +-
.../src/gatb/tools/compression/RangeCoder.hpp | 4 +-
gatb-core/src/gatb/tools/designpattern/.DS_Store | Bin 6148 -> 0 bytes
.../src/gatb/tools/designpattern/api/.DS_Store | Bin 6148 -> 0 bytes
.../src/gatb/tools/designpattern/api/Iterator.hpp | 12 +-
.../src/gatb/tools/designpattern/impl/.DS_Store | Bin 6148 -> 0 bytes
.../tools/designpattern/impl/IteratorHelpers.hpp | 60 +-
gatb-core/src/gatb/tools/misc/.DS_Store | Bin 8196 -> 0 bytes
gatb-core/src/gatb/tools/misc/api/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/src/gatb/tools/misc/api/IHistogram.hpp | 5 +
gatb-core/src/gatb/tools/misc/impl/.DS_Store | Bin 8196 -> 0 bytes
gatb-core/src/gatb/tools/misc/impl/Histogram.cpp | 15 +
gatb-core/src/gatb/tools/misc/impl/Histogram.hpp | 16 +-
gatb-core/src/gatb/tools/misc/impl/Pool.hpp | 34 +-
gatb-core/src/gatb/tools/misc/impl/Stringify.hpp | 4 +
gatb-core/src/gatb/tools/misc/impl/Tool.cpp | 2 +-
gatb-core/src/gatb/tools/storage/impl/Storage.cpp | 285 +++
gatb-core/src/gatb/tools/storage/impl/Storage.hpp | 98 +-
gatb-core/src/gatb/tools/storage/impl/Storage.tpp | 4 +-
.../src/gatb/tools/storage/impl/StorageHDF5.hpp | 20 +-
.../db/NIST7035_TAAGGCGA_L001_R1_001_5OK.fastq.gz | Bin 0 -> 3891060 bytes
...IST7035_TAAGGCGA_L001_R1_001_5OK.fastq.leon-ref | Bin 0 -> 3276064 bytes
gatb-core/test/db/README.md | 22 +
gatb-core/test/db/giab.hg002.2D_6K.fastq.gz | Bin 0 -> 23908774 bytes
gatb-core/test/db/{sample.fastq => leon1.fastq} | 0
gatb-core/test/db/leon1.fastq.leon-ref | Bin 0 -> 134856 bytes
gatb-core/test/db/{sample.fastq => leon2.fastq} | 0
gatb-core/test/db/leon2.fastq.leon-ref | Bin 0 -> 134856 bytes
gatb-core/test/jenkins/leon/README.md | 62 +
gatb-core/test/jenkins/leon/download.sh | 72 +
gatb-core/test/jenkins/leon/test_integrity.sh | 31 +
.../tool-leon-functional-tests-compile.sh} | 53 +-
.../leon/tool-leon-functional-tests-test.sh | 266 +++
gatb-core/test/jenkins/publish-doc-api.sh | 20 +-
.../jenkins/test-bin-debian7-64bits-gcc-4.7.sh | 12 +-
...cc-4.2.1 => test-bin-macos-10.9.5-gcc-4.2.1.sh} | 12 +-
.../test-docker-gatb-core-compile-clang36.sh | 42 +
.../test-snippets-debian7-64bits-gcc-4.7.sh | 4 +-
.../test/jenkins/test-suite-fedora20-gcc-4.8.sh | 6 +-
.../test/slaves/ubuntu16-shell-provisioner.sh | 99 +
gatb-core/test/unit/src/bank/TestBank.cpp | 2 +-
gatb-core/test/unit/src/bank/TestLeon.cpp | 435 ++++
gatb-core/test/unit/src/debruijn/TestDebruijn.cpp | 2 +-
.../src/debruijn/TestSimplificationsUnitigs.cpp | 65 +-
gatb-core/test/unit/src/kmer/TestDSK.cpp | 4 +-
gatb-core/test/unit/src/kmer/TestMPHF.cpp | 7 +-
gatb-core/test/unit/src/main.cpp | 28 +-
.../test/unit/src/tools/collections/TestMap.cpp | 10 +-
gatb-core/thirdparty/json/json.hpp | 659 ++++++
gatb-core/tools/CMakeLists.txt | 4 +-
gatb-core/tools/dbgh5.cpp | 2 +-
gatb-core/tools/{dbginfo.cpp => leon.cpp} | 59 +-
142 files changed, 14742 insertions(+), 2117 deletions(-)
create mode 100644 .travis.yml
delete mode 100644 gatb-core/cmake/GetDate.cmake
delete mode 100644 gatb-core/examples/.DS_Store
create mode 100644 gatb-core/examples/Makefile
create mode 100644 gatb-core/examples/README.md
create mode 100644 gatb-core/examples/bank/bank21.cpp
create mode 100644 gatb-core/examples/bank/bank22.cpp
copy gatb-core/examples/bank/{bank15.cpp => bank23.cpp} (74%)
create mode 100644 gatb-core/examples/bank/bank24.cpp
create mode 100644 gatb-core/examples/bank/bank25.cpp
copy gatb-core/examples/bank/{bank2.cpp => bank26.cpp} (75%)
copy gatb-core/examples/bank/{bank14.cpp => bank27.cpp} (64%)
copy gatb-core/examples/bank/{bank14.cpp => bank28.cpp} (68%)
delete mode 100644 gatb-core/examples/kmer/.DS_Store
delete mode 100644 gatb-core/examples/storage/.DS_Store
copy gatb-core/examples/tools/{multithreading6.cpp => multithreading8.cpp} (59%)
delete mode 100644 gatb-core/src/.DS_Store
delete mode 100644 gatb-core/src/gatb/.DS_Store
delete mode 100644 gatb-core/src/gatb/bank/.DS_Store
delete mode 100644 gatb-core/src/gatb/bank/api/.DS_Store
delete mode 100644 gatb-core/src/gatb/bcalm2/lockstdqueue.h
create mode 100644 gatb-core/src/gatb/bcalm2/logging.cpp
create mode 100644 gatb-core/src/gatb/bcalm2/logging.hpp
create mode 100644 gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp
copy gatb-core/src/gatb/{system/api/config.hpp.in => debruijn/impl/LinkTigs.hpp} (60%)
create mode 100644 gatb-core/src/gatb/debruijn/impl/dag_vector.hpp
create mode 100644 gatb-core/src/gatb/debruijn/impl/rank_vector.hpp
delete mode 100644 gatb-core/src/gatb/kmer/.DS_Store
delete mode 100644 gatb-core/src/gatb/kmer/impl/.DS_Store
delete mode 100644 gatb-core/src/gatb/tools/.DS_Store
create mode 100644 gatb-core/src/gatb/tools/compression/DnaCoder.cpp
create mode 100644 gatb-core/src/gatb/tools/compression/DnaCoder.hpp
create mode 100644 gatb-core/src/gatb/tools/compression/HeaderCoder.cpp
create mode 100644 gatb-core/src/gatb/tools/compression/HeaderCoder.hpp
create mode 100644 gatb-core/src/gatb/tools/compression/Leon.cpp
create mode 100644 gatb-core/src/gatb/tools/compression/Leon.hpp
delete mode 100644 gatb-core/src/gatb/tools/designpattern/.DS_Store
delete mode 100644 gatb-core/src/gatb/tools/designpattern/api/.DS_Store
delete mode 100644 gatb-core/src/gatb/tools/designpattern/impl/.DS_Store
delete mode 100644 gatb-core/src/gatb/tools/misc/.DS_Store
delete mode 100644 gatb-core/src/gatb/tools/misc/api/.DS_Store
delete mode 100644 gatb-core/src/gatb/tools/misc/impl/.DS_Store
create mode 100644 gatb-core/test/db/NIST7035_TAAGGCGA_L001_R1_001_5OK.fastq.gz
create mode 100644 gatb-core/test/db/NIST7035_TAAGGCGA_L001_R1_001_5OK.fastq.leon-ref
create mode 100644 gatb-core/test/db/README.md
create mode 100644 gatb-core/test/db/giab.hg002.2D_6K.fastq.gz
copy gatb-core/test/db/{sample.fastq => leon1.fastq} (100%)
create mode 100644 gatb-core/test/db/leon1.fastq.leon-ref
copy gatb-core/test/db/{sample.fastq => leon2.fastq} (100%)
create mode 100644 gatb-core/test/db/leon2.fastq.leon-ref
create mode 100644 gatb-core/test/jenkins/leon/README.md
create mode 100755 gatb-core/test/jenkins/leon/download.sh
create mode 100755 gatb-core/test/jenkins/leon/test_integrity.sh
copy gatb-core/test/jenkins/{publish-doc-api.sh => leon/tool-leon-functional-tests-compile.sh} (66%)
create mode 100755 gatb-core/test/jenkins/leon/tool-leon-functional-tests-test.sh
rename gatb-core/test/jenkins/{test-bin-macos-10.9.5-gcc-4.2.1 => test-bin-macos-10.9.5-gcc-4.2.1.sh} (89%)
create mode 100755 gatb-core/test/jenkins/test-docker-gatb-core-compile-clang36.sh
create mode 100755 gatb-core/test/slaves/ubuntu16-shell-provisioner.sh
create mode 100644 gatb-core/test/unit/src/bank/TestLeon.cpp
create mode 100644 gatb-core/thirdparty/json/json.hpp
copy gatb-core/tools/{dbginfo.cpp => leon.cpp} (56%)
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