[med-svn] [gatb-core] 03/04: Updated version 1.4.0+dfsg from 'upstream/1.4.0+dfsg'
Andreas Tille
tille at debian.org
Fri Dec 1 14:31:38 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository gatb-core.
commit 9c7180d40e137e9b471429b1b3ed4340d09acef2
Merge: e30bf58 51eb9b0
Author: Andreas Tille <tille at debian.org>
Date: Fri Dec 1 15:24:20 2017 +0100
Updated version 1.4.0+dfsg from 'upstream/1.4.0+dfsg'
with Debian dir b518a4f4174d1ea08015b5a3c88204b7e295efee
.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/bank26.cpp | 54 +
gatb-core/examples/bank/bank27.cpp | 70 +
gatb-core/examples/bank/bank28.cpp | 64 +
gatb-core/examples/kmer/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/examples/storage/.DS_Store | Bin 6148 -> 0 bytes
gatb-core/examples/tools/multithreading8.cpp | 89 +
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 +++
gatb-core/src/gatb/debruijn/impl/LinkTigs.hpp | 40 +
.../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/leon1.fastq | 28 +
gatb-core/test/db/leon1.fastq.leon-ref | Bin 0 -> 134856 bytes
gatb-core/test/db/leon2.fastq | 28 +
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/leon.cpp | 61 +
142 files changed, 15051 insertions(+), 2028 deletions(-)
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