[med-svn] [bedops] branch upstream updated (11a80e0 -> eabeaa5)
Olivier Sallou
osallou at debian.org
Wed Jun 21 12:27:24 UTC 2017
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osallou pushed a change to branch upstream
in repository bedops.
from 11a80e0 Import Upstream version 2.4.20+dfsg
new eabeaa5 New upstream version 2.4.26+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:
.gitignore | 63 +
.travis.yml | 34 +-
Makefile | 52 +-
README.md | 22 +-
applications/bed/bedextract/src/ExtractRows.cpp | 2 +-
applications/bed/bedmap/src/Bedmap.cpp | 38 +-
applications/bed/bedmap/src/Input.hpp | 25 +-
applications/bed/bedmap/src/TDefs.hpp | 23 +-
applications/bed/bedops/src/BedPadReader.hpp | 2 +-
applications/bed/bedops/src/Bedops.cpp | 30 +-
applications/bed/bedops/src/Input.hpp | 2 +-
applications/bed/bedops/src/Makefile.darwin | 2 +-
applications/bed/bedops/test/Regression.java | 2 +-
applications/bed/bedops/test/TestPlan.xml | 55 +
.../closestfeats/doc/Usage.Statement.Version1.2 | 45 -
applications/bed/closestfeats/src/BedReader.hpp | 2 +-
.../bed/closestfeats/src/ClosestFeature.cpp | 2 +-
applications/bed/closestfeats/src/Input.hpp | 2 +-
applications/bed/closestfeats/src/Printers.hpp | 2 +-
applications/bed/conversion/src/convert2bed.c | 2577 +++++++++++++++-----
applications/bed/conversion/src/convert2bed.h | 101 +-
.../src/wrappers/{bam2bed_sge => bam2bed_slurm} | 33 +-
.../src/wrappers/{bam2bed_sge => bam2starch_slurm} | 33 +-
applications/bed/sort-bed/src/CheckSort.cpp | 2 +-
applications/bed/sort-bed/src/Makefile | 14 +-
applications/bed/sort-bed/src/Makefile.darwin | 11 +-
applications/bed/sort-bed/src/Sort.cpp | 2 +-
applications/bed/sort-bed/src/SortDetails.cpp | 50 +-
applications/bed/sort-bed/src/Structures.hpp | 49 +-
.../src/update-sort-bed-migrate-candidates.py | 613 +++++
.../bed/sort-bed/src/update-sort-bed-slurm.py | 426 ++++
.../sort-bed/src/update-sort-bed-starch-slurm.py | 462 ++++
applications/bed/starch/src/Makefile | 16 +-
applications/bed/starch/src/Makefile.darwin | 25 +-
applications/bed/starch/src/starch-diff.py | 213 ++
applications/bed/starch/src/starch.c | 104 +-
applications/bed/starch/src/starch.h | 65 +-
applications/bed/starch/src/starchcat.c | 1415 +++++++----
applications/bed/starch/src/starchcat.h | 85 +-
.../bed/starch/src/starchcluster_gnuParallel.tcsh | 4 +-
applications/bed/starch/src/starchcluster_sge.tcsh | 4 +-
...chcluster_sge.tcsh => starchcluster_slurm.tcsh} | 37 +-
applications/bed/starch/src/starchstrip.c | 898 +++++++
applications/bed/starch/src/starchstrip.h | 143 ++
applications/bed/starch/src/unstarch.c | 285 ++-
applications/bed/starch/src/unstarch.h | 113 +-
docs/_static/custom.css | 12 +-
docs/conf.py | 8 +-
.../reference/file-management/compression.rst | 3 +
.../file-management/compression/starch-diff.rst | 52 +
.../compression/starch-specification.rst | 16 +-
.../file-management/compression/starch.rst | 61 +-
.../file-management/compression/starchcat.rst | 57 +-
.../file-management/compression/starchstrip.rst | 101 +
.../file-management/compression/unstarch.rst | 156 +-
.../file-management/conversion/gtf2bed.rst | 12 +-
.../conversion/parallel_bam2bed.rst | 12 +-
.../conversion/parallel_bam2starch.rst | 10 +-
.../file-management/conversion/psl2bed.rst | 2 +-
.../file-management/conversion/vcf2bed.rst | 2 +-
.../reference/file-management/sorting/sort-bed.rst | 22 +-
.../reference/set-operations/bedextract.rst | 2 +-
docs/content/reference/set-operations/bedops.rst | 2 +-
.../reference/set-operations/closest-features.rst | 2 +-
docs/content/reference/statistics/bedmap.rst | 23 +-
docs/content/release.rst | 8 +-
docs/content/revision-history.rst | 451 +++-
docs/content/summary.rst | 133 +-
docs/content/usage-examples/starchcluster.rst | 6 +-
docs/index.rst | 26 +-
.../general-headers/algorithm/WindowSweep.hpp | 6 +-
.../general-headers/algorithm/bed/FindBedRange.hpp | 2 +-
.../algorithm/visitors/BedVisitors.hpp | 3 +-
.../algorithm/visitors/NumericalVisitors.hpp | 2 +-
.../algorithm/visitors/OtherVisitors.hpp | 2 +-
.../algorithm/visitors/VisitorFactory.hpp | 2 +-
.../algorithm/visitors/Visitors.hpp | 2 +-
.../algorithm/visitors/bed/BedBaseVisitor.hpp | 4 +-
.../algorithm/visitors/bed/EchoMapBedVisitor.hpp | 2 +-
.../visitors/bed/EchoMapIntersectLengthVisitor.hpp | 5 +-
.../algorithm/visitors/bed/OvrAggregateVisitor.hpp | 2 +-
.../visitors/bed/OvrUniqueFractionVisitor.hpp | 2 +-
.../algorithm/visitors/bed/OvrUniqueVisitor.hpp | 2 +-
.../WeightedAverageVisitor.hpp} | 53 +-
.../algorithm/visitors/helpers/NamedVisitors.hpp | 65 +-
.../visitors/helpers/ProcessBedVisitorRow.hpp | 2 +-
.../visitors/helpers/ProcessVisitorRow.hpp | 2 +-
.../visitors/numerical/AverageVisitor.hpp | 2 +-
.../visitors/numerical/CoeffVariationVisitor.hpp | 2 +-
.../algorithm/visitors/numerical/CountVisitor.hpp | 2 +-
.../visitors/numerical/ExtremeVisitor.hpp | 69 +-
.../visitors/numerical/IndicatorVisitor.hpp | 2 +-
.../numerical/MedianAbsoluteDeviationVisitor.hpp | 2 +-
.../algorithm/visitors/numerical/MedianVisitor.hpp | 2 +-
.../numerical/RollingKthAverageVisitor.hpp | 2 +-
.../visitors/numerical/RollingKthVisitor.hpp | 2 +-
.../algorithm/visitors/numerical/StdevVisitor.hpp | 2 +-
.../algorithm/visitors/numerical/SumVisitor.hpp | 2 +-
.../visitors/numerical/TrimmedMeanVisitor.hpp | 2 +-
.../visitors/numerical/VarianceVisitor.hpp | 2 +-
.../algorithm/visitors/other/EchoVisitor.hpp | 2 +-
.../algorithm/visitors/other/MultiVisitor.hpp | 2 +-
.../data/bed/AllocateIterator_BED_starch.hpp | 5 +-
interfaces/general-headers/data/bed/Bed.hpp | 331 +--
.../general-headers/data/bed/BedCheckIterator.hpp | 78 +-
interfaces/general-headers/data/bed/BedCompare.hpp | 130 +-
.../general-headers/data/bed/BedDistances.hpp | 2 +-
interfaces/general-headers/data/bed/BedTypes.hpp | 9 +-
.../data/measurement/AssayMeasurement.hpp | 2 +-
.../general-headers/data/measurement/NaN.hpp | 2 +-
.../data/measurement/SelectMeasureType.hpp | 2 +-
.../general-headers/data/starch/starchApi.hpp | 55 +-
.../data/starch/starchBase64Coding.h | 2 +-
.../general-headers/data/starch/starchConstants.h | 2 +-
.../data/starch/starchFileHelpers.h | 20 +-
.../general-headers/data/starch/starchHelpers.h | 17 +-
.../data/starch/starchMetadataHelpers.h | 40 +-
.../general-headers/data/starch/starchSha1Digest.h | 6 +-
.../general-headers/data/starch/unstarchHelpers.h | 57 +-
.../general-headers/suite/BEDOPS.Constants.hpp | 30 +-
.../general-headers/suite/BEDOPS.Version.hpp | 4 +-
.../general-headers/utility/AllocateIterator.hpp | 2 +-
interfaces/general-headers/utility/Assertion.hpp | 2 +-
interfaces/general-headers/utility/ByLine.hpp | 2 +-
interfaces/general-headers/utility/Exception.hpp | 2 +-
interfaces/general-headers/utility/FPWrap.hpp | 2 +-
interfaces/general-headers/utility/Factory.hpp | 2 +-
interfaces/general-headers/utility/Formats.hpp | 2 +-
.../general-headers/utility/IteratorPair.hpp | 2 +-
.../general-headers/utility/OrderCompare.hpp | 2 +-
.../general-headers/utility/PooledMemory.hpp | 508 ++++
interfaces/general-headers/utility/PrintTypes.hpp | 2 +-
.../general-headers/utility/SingletonType.hpp | 2 +-
interfaces/general-headers/utility/Typify.hpp | 2 +-
interfaces/src/algorithm/sweep/WindowSweepImpl.cpp | 2 +-
.../algorithm/sweep/WindowSweepImpl.specialize.cpp | 2 +-
interfaces/src/data/measurement/NaN.cpp | 2 +-
interfaces/src/data/starch/starchBase64Coding.c | 2 +-
interfaces/src/data/starch/starchConstants.c | 2 +-
interfaces/src/data/starch/starchFileHelpers.c | 2 +-
interfaces/src/data/starch/starchHelpers.c | 442 +++-
interfaces/src/data/starch/starchMetadataHelpers.c | 316 ++-
interfaces/src/data/starch/unstarchHelpers.c | 434 +++-
packaging/deb/Dockerfile | 8 +-
packaging/deb/control | 2 +-
packaging/os_x/BEDOPS.pkgproj | 139 +-
packaging/rpm/Dockerfile | 12 +-
packaging/rpm/bedops.spec | 2 +-
system.mk/Makefile.darwin | 21 +
system.mk/Makefile.linux | 15 +
150 files changed, 9923 insertions(+), 2425 deletions(-)
create mode 100644 .gitignore
delete mode 100644 applications/bed/closestfeats/doc/Usage.Statement.Version1.2
copy applications/bed/conversion/src/wrappers/{bam2bed_sge => bam2bed_slurm} (85%)
copy applications/bed/conversion/src/wrappers/{bam2bed_sge => bam2starch_slurm} (85%)
create mode 100755 applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
create mode 100755 applications/bed/sort-bed/src/update-sort-bed-slurm.py
create mode 100755 applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
create mode 100755 applications/bed/starch/src/starch-diff.py
copy applications/bed/starch/src/{starchcluster_sge.tcsh => starchcluster_slurm.tcsh} (82%)
create mode 100644 applications/bed/starch/src/starchstrip.c
create mode 100644 applications/bed/starch/src/starchstrip.h
create mode 100644 docs/content/reference/file-management/compression/starch-diff.rst
create mode 100644 docs/content/reference/file-management/compression/starchstrip.rst
copy interfaces/general-headers/algorithm/visitors/{numerical/AverageVisitor.hpp => bed/WeightedAverageVisitor.hpp} (60%)
create mode 100644 interfaces/general-headers/utility/PooledMemory.hpp
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