[med-svn] [unanimity] branch upstream updated (02c66a5 -> a9e5d64)
Afif Elghraoui
afif at moszumanska.debian.org
Fri Feb 3 08:03:15 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository unanimity.
from 02c66a5 Imported Upstream version 2.0.4+20161206+dfsg
new a9e5d64 Imported Upstream version 2.1.0~20160130+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:
.gitattributes | 2 +
.gitmodules | 2 +-
CHANGELOG.md | 10 +
CMakeLists.txt | 4 +-
README.md | 27 +-
cmake/uny-compilerflags.cmake | 6 +-
cmake/uny-dependencies.cmake | 3 +
doc/CLERIC.md | 37 +
doc/FUSE.md | 33 +
doc/JULIET.md | 125 +++
doc/JULIETFLOW.md | 36 +
doc/img/cleric.png | Bin 0 -> 7926 bytes
doc/img/fuse.png | Bin 0 -> 12677 bytes
doc/img/juliet.png | Bin 0 -> 180047 bytes
doc/img/juliet_hiv-hiv.png | Bin 0 -> 71897 bytes
doc/img/juliet_hiv-own.png | Bin 0 -> 53046 bytes
doc/img/juliet_hiv-unknown.png | Bin 0 -> 43879 bytes
doc/img/julietflow.png | Bin 0 -> 140452 bytes
.../{data/Sequence.h => align/SimdAlignment.h} | 18 +-
include/pacbio/ccs/Consensus.h | 2 +-
include/pacbio/consensus/AbstractIntegrator.h | 2 +-
include/pacbio/data/{Sequence.h => ArrayBase.h} | 39 +-
include/pacbio/data/ArrayRead.h | 145 +++
include/pacbio/data/{Sequence.h => FisherResult.h} | 21 +-
.../pacbio/{consensus/ModelConfig.h => data/MSA.h} | 91 +-
include/pacbio/data/MSAColumn.h | 115 +++
include/pacbio/{Version.h.in => io/BamParser.h} | 47 +-
include/pacbio/io/Utility.h | 2 +
include/pacbio/juliet/AminoAcidCaller.h | 174 ++++
.../{data/StrandType.h => juliet/AnalysisMode.h} | 19 +-
.../{Version.h.in => juliet/ErrorEstimates.h} | 43 +-
.../{Version.h.in => juliet/JulietSettings.h} | 55 +-
.../JulietWorkflow.h} | 23 +-
include/pacbio/juliet/ResistanceCaller.h | 122 +++
.../pacbio/{Version.h.in => juliet/TargetConfig.h} | 66 +-
include/pacbio/realign/Cleric.h | 97 ++
.../ClericSettings.h} | 28 +-
include/pacbio/{Version.h.in => realign/Fuse.h} | 47 +-
.../{Version.h.in => realign/FuseSettings.h} | 44 +-
include/pacbio/statistics/Fisher.h | 26 +
.../{exception/StateError.h => statistics/Tests.h} | 51 +-
include/pacbio/util/Timer.h | 2 +
scripts/ci/build.sh | 47 +-
scripts/minorvariant/build.sh | 19 +
scripts/minorvariant/julietflow | 73 ++
scripts/nightly/build.sh | 2 +-
src/AminoAcidCaller.cpp | 612 ++++++++++++
src/ArrayRead.cpp | 143 +++
src/CMakeLists.txt | 75 +-
src/Cleric.cpp | 745 ++++++++++++++
.../ConsensusSettings.h => src/ClericSettings.cpp | 103 +-
.../pacbio/Version.h.in => src/ErrorEstimates.cpp | 49 +-
src/Fisher.cpp | 192 ++++
src/Fuse.cpp | 153 +++
src/FuseSettings.cpp | 139 +++
src/JulietSettings.cpp | 220 +++++
src/JulietWorkflow.cpp | 194 ++++
src/MSA.cpp | 267 +++++
.../pacbio/data/Sequence.h => src/MSAColumn.cpp | 33 +-
src/Polish.cpp | 18 +-
src/ResistanceCaller.cpp | 679 +++++++++++++
src/SimdAlignment.cpp | 122 +++
src/TargetConfig.cpp | 166 ++++
src/Tests.cpp | 126 +++
src/Timer.cpp | 26 +-
src/Utility.cpp | 17 +
src/main/cleric.cpp | 141 +++
include/pacbio/Version.h.in => src/main/fuse.cpp | 61 +-
include/pacbio/Version.h.in => src/main/juliet.cpp | 48 +-
src/{ModelConfig.cpp => models/CounterWeight.h} | 53 +-
src/models/MarginalModelForm.cpp | 27 +-
src/models/P6C4NoCovModel.cpp | 99 +-
src/models/PwSnrAModelForm.cpp | 26 +-
src/models/PwSnrModelForm.cpp | 26 +-
src/models/S_P1C1Beta_Model.cpp | 37 +-
src/models/S_P1C1v1_Model.cpp | 37 +-
src/models/S_P1C1v2_Model.cpp | 58 +-
src/models/S_P2C2_Model.cpp | 395 --------
src/models/SnrModelForm.cpp | 29 +-
src/poa/PoaGraphImpl.cpp | 34 +-
tests/CMakeLists.txt | 4 +-
tests/cram/100zmws.t | 302 +++---
tests/cram/100zmws_byStrand.t | 667 +++++++------
tests/cram/fuse.t | 23 +
tests/cram/internal/big.t | 2 +-
tests/cram/juliet.t | 11 +
tests/cram/nozfilter.t | 4 +-
tests/cram/siv/julietflow.t | 13 +
tests/cram/tiny.t | 6 +-
tests/data/fuse/doubleCodonMissing.bam | Bin 0 -> 818 bytes
tests/data/fuse/doubleCodonMissing.fasta | 2 +
tests/data/fuse/doubleCodonMissingTruth.fasta | 2 +
tests/data/fuse/gaps.bam | Bin 0 -> 876 bytes
tests/data/fuse/gaps.fasta | 2 +
tests/data/fuse/identical.bam | Bin 0 -> 767 bytes
tests/data/fuse/identicalref.fasta | 2 +
tests/data/fuse/singleCodonMissing.bam | Bin 0 -> 809 bytes
tests/data/fuse/singleCodonMissing.fasta | 2 +
tests/data/juliet_hiv_3000_96-1-1-1-1.align.bam | Bin 0 -> 9102430 bytes
tests/data/juliet_hiv_3000_97-1-1-1.align.bam | Bin 0 -> 8936079 bytes
tests/data/julietflow/flea99_97_1.bam | 3 +
tests/data/julietflow/hxb2.fasta | 3 +
tests/data/julietflow/sb99_96_1.bam | 3 +
tests/data/params/SP1C1Beta.json | 3 +-
tests/data/params/SP1C1v1.json | 3 +-
tests/data/params/SP1C1v2.json | 3 +-
tests/data/params/SP2C2.json | 1026 --------------------
tests/python/test_tool_contract.py | 4 +-
tests/unit/FisherTest.cpp | 74 ++
tests/unit/RandomDNA.cpp | 12 +-
tests/unit/RandomDNA.h | 2 +-
tests/unit/TestIntegrator.cpp | 34 +-
tests/unit/TestLoadModels.cpp | 27 +-
third-party/cssw/ssw.c | 981 +++++++++++++++++++
third-party/cssw/ssw.h | 188 ++++
third-party/cssw/ssw_cpp.cpp | 476 +++++++++
third-party/cssw/ssw_cpp.h | 219 +++++
tools/check-formatting | 34 +
tools/format-all | 9 +
tools/git-clang-format | 485 +++++++++
120 files changed, 8969 insertions(+), 2517 deletions(-)
create mode 100644 .gitattributes
create mode 100644 doc/CLERIC.md
create mode 100644 doc/FUSE.md
create mode 100644 doc/JULIET.md
create mode 100644 doc/JULIETFLOW.md
create mode 100644 doc/img/cleric.png
create mode 100644 doc/img/fuse.png
create mode 100644 doc/img/juliet.png
create mode 100644 doc/img/juliet_hiv-hiv.png
create mode 100644 doc/img/juliet_hiv-own.png
create mode 100644 doc/img/juliet_hiv-unknown.png
create mode 100644 doc/img/julietflow.png
copy include/pacbio/{data/Sequence.h => align/SimdAlignment.h} (84%)
copy include/pacbio/data/{Sequence.h => ArrayBase.h} (64%)
create mode 100644 include/pacbio/data/ArrayRead.h
copy include/pacbio/data/{Sequence.h => FisherResult.h} (88%)
copy include/pacbio/{consensus/ModelConfig.h => data/MSA.h} (56%)
create mode 100644 include/pacbio/data/MSAColumn.h
copy include/pacbio/{Version.h.in => io/BamParser.h} (63%)
create mode 100644 include/pacbio/juliet/AminoAcidCaller.h
copy include/pacbio/{data/StrandType.h => juliet/AnalysisMode.h} (89%)
copy include/pacbio/{Version.h.in => juliet/ErrorEstimates.h} (72%)
copy include/pacbio/{Version.h.in => juliet/JulietSettings.h} (62%)
copy include/pacbio/{exception/InvalidEvaluatorException.h => juliet/JulietWorkflow.h} (83%)
create mode 100644 include/pacbio/juliet/ResistanceCaller.h
copy include/pacbio/{Version.h.in => juliet/TargetConfig.h} (62%)
create mode 100644 include/pacbio/realign/Cleric.h
copy include/pacbio/{exception/InvalidEvaluatorException.h => realign/ClericSettings.h} (75%)
copy include/pacbio/{Version.h.in => realign/Fuse.h} (67%)
copy include/pacbio/{Version.h.in => realign/FuseSettings.h} (69%)
create mode 100644 include/pacbio/statistics/Fisher.h
copy include/pacbio/{exception/StateError.h => statistics/Tests.h} (68%)
create mode 100644 scripts/minorvariant/build.sh
create mode 100755 scripts/minorvariant/julietflow
create mode 100644 src/AminoAcidCaller.cpp
create mode 100644 src/ArrayRead.cpp
create mode 100644 src/Cleric.cpp
copy include/pacbio/ccs/ConsensusSettings.h => src/ClericSettings.cpp (51%)
copy include/pacbio/Version.h.in => src/ErrorEstimates.cpp (66%)
create mode 100644 src/Fisher.cpp
create mode 100644 src/Fuse.cpp
create mode 100644 src/FuseSettings.cpp
create mode 100644 src/JulietSettings.cpp
create mode 100644 src/JulietWorkflow.cpp
create mode 100644 src/MSA.cpp
copy include/pacbio/data/Sequence.h => src/MSAColumn.cpp (70%)
create mode 100644 src/ResistanceCaller.cpp
create mode 100644 src/SimdAlignment.cpp
create mode 100644 src/TargetConfig.cpp
create mode 100644 src/Tests.cpp
create mode 100644 src/main/cleric.cpp
copy include/pacbio/Version.h.in => src/main/fuse.cpp (57%)
copy include/pacbio/Version.h.in => src/main/juliet.cpp (70%)
copy src/{ModelConfig.cpp => models/CounterWeight.h} (57%)
delete mode 100644 src/models/S_P2C2_Model.cpp
create mode 100644 tests/cram/fuse.t
create mode 100644 tests/cram/juliet.t
create mode 100644 tests/cram/siv/julietflow.t
create mode 100644 tests/data/fuse/doubleCodonMissing.bam
create mode 100644 tests/data/fuse/doubleCodonMissing.fasta
create mode 100644 tests/data/fuse/doubleCodonMissingTruth.fasta
create mode 100644 tests/data/fuse/gaps.bam
create mode 100644 tests/data/fuse/gaps.fasta
create mode 100644 tests/data/fuse/identical.bam
create mode 100644 tests/data/fuse/identicalref.fasta
create mode 100644 tests/data/fuse/singleCodonMissing.bam
create mode 100644 tests/data/fuse/singleCodonMissing.fasta
create mode 100644 tests/data/juliet_hiv_3000_96-1-1-1-1.align.bam
create mode 100644 tests/data/juliet_hiv_3000_97-1-1-1.align.bam
create mode 100644 tests/data/julietflow/flea99_97_1.bam
create mode 100644 tests/data/julietflow/hxb2.fasta
create mode 100644 tests/data/julietflow/sb99_96_1.bam
delete mode 100644 tests/data/params/SP2C2.json
create mode 100644 tests/unit/FisherTest.cpp
create mode 100644 third-party/cssw/ssw.c
create mode 100644 third-party/cssw/ssw.h
create mode 100644 third-party/cssw/ssw_cpp.cpp
create mode 100644 third-party/cssw/ssw_cpp.h
create mode 100755 tools/check-formatting
create mode 100755 tools/format-all
create mode 100755 tools/git-clang-format
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