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osallou pushed a change to branch master
in repository bedops.
from 100f21f Fix upstream metadata
new eabeaa5 New upstream version 2.4.26+dfsg
new 060e566 Merge tag 'upstream/2.4.26+dfsg'
new f7ae470 new upstream release 2.4.26+dfsg
new ecd23a9 fix debian patch for new release
new 3b74f7b prepare new release, need to fix call to cdn library
instead of local library in html doc
The 5 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 +-
debian/changelog | 10 +
debian/control | 2 +
debian/patches/use_debian_libs | 21 +-
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 +
153 files changed, 9941 insertions(+), 2440 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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