[med-svn] [Git][med-team/bedops][upstream] New upstream version 2.4.42+dfsg

Sun Aug 17 23:29:11 BST 2025

Steffen Möller pushed to branch upstream at Debian Med / bedops

Commits:
d714ec38 by Steffen Moeller at 2025-08-18T00:04:43+02:00
New upstream version 2.4.42+dfsg
- - - - -

139 changed files:

- CHANGELOG.md
- CITATION.cff
- Makefile
- README.md
- applications/bed/bedextract/src/ExtractRows.cpp
- applications/bed/bedmap/src/Bedmap.cpp
- applications/bed/bedmap/src/Input.hpp
- applications/bed/bedmap/src/TDefs.hpp
- applications/bed/bedops/src/BedPadReader.hpp
- applications/bed/bedops/src/Bedops.cpp
- applications/bed/bedops/src/Input.hpp
- applications/bed/closestfeats/src/BedReader.hpp
- applications/bed/closestfeats/src/ClosestFeature.cpp
- applications/bed/closestfeats/src/Input.hpp
- applications/bed/closestfeats/src/Printers.hpp
- applications/bed/conversion/src/convert2bed.c
- applications/bed/conversion/src/convert2bed.h
- applications/bed/sort-bed/src/CheckSort.cpp
- applications/bed/sort-bed/src/Sort.cpp
- applications/bed/sort-bed/src/SortDetails.cpp
- applications/bed/sort-bed/src/Structures.hpp
- applications/bed/sort-bed/src/update-sort-bed-migrate-candidates.py
- applications/bed/sort-bed/src/update-sort-bed-slurm.py
- applications/bed/sort-bed/src/update-sort-bed-starch-slurm.py
- applications/bed/starch/src/Makefile.darwin
- applications/bed/starch/src/starch-diff.py
- applications/bed/starch/src/starch.c
- applications/bed/starch/src/starch.h
- applications/bed/starch/src/starchcat.c
- applications/bed/starch/src/starchcat.h
- applications/bed/starch/src/starchcluster_gnuParallel.tcsh
- applications/bed/starch/src/starchcluster_sge.tcsh
- applications/bed/starch/src/starchcluster_slurm.tcsh
- applications/bed/starch/src/starchstrip.c
- applications/bed/starch/src/starchstrip.h
- applications/bed/starch/src/unstarch.c
- applications/bed/starch/src/unstarch.h
- docs/conf.py
- docs/content/reference/file-management/compression/starch-diff.rst
- docs/content/reference/file-management/compression/starch.rst
- docs/content/reference/file-management/compression/starchcat.rst
- docs/content/reference/file-management/compression/starchstrip.rst
- docs/content/reference/file-management/compression/unstarch.rst
- docs/content/reference/file-management/conversion/gtf2bed.rst
- docs/content/reference/file-management/conversion/psl2bed.rst
- docs/content/reference/file-management/conversion/vcf2bed.rst
- docs/content/reference/file-management/sorting/sort-bed.rst
- docs/content/reference/set-operations/bedextract.rst
- docs/content/reference/set-operations/bedops.rst
- docs/content/reference/set-operations/closest-features.rst
- docs/content/reference/statistics/bedmap.rst
- docs/content/release.rst
- docs/content/revision-history.rst
- docs/content/usage-examples/snps-within-dhses.rst
- docs/index.rst
- .readthedocs.yml → docs/readthedocs.yaml
- interfaces/general-headers/algorithm/WindowSweep.hpp
- interfaces/general-headers/algorithm/bed/FindBedRange.hpp
- interfaces/general-headers/algorithm/visitors/BedVisitors.hpp
- interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp
- interfaces/general-headers/algorithm/visitors/OtherVisitors.hpp
- interfaces/general-headers/algorithm/visitors/VisitorFactory.hpp
- interfaces/general-headers/algorithm/visitors/Visitors.hpp
- interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp
- interfaces/general-headers/algorithm/visitors/bed/EchoMapBedVisitor.hpp
- interfaces/general-headers/algorithm/visitors/bed/EchoMapIntersectLengthVisitor.hpp
- interfaces/general-headers/algorithm/visitors/bed/OvrAggregateVisitor.hpp
- interfaces/general-headers/algorithm/visitors/bed/OvrUniqueFractionVisitor.hpp
- interfaces/general-headers/algorithm/visitors/bed/OvrUniqueVisitor.hpp
- interfaces/general-headers/algorithm/visitors/bed/WeightedAverageVisitor.hpp
- interfaces/general-headers/algorithm/visitors/helpers/NamedVisitors.hpp
- interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp
- interfaces/general-headers/algorithm/visitors/helpers/ProcessVisitorRow.hpp
- interfaces/general-headers/algorithm/visitors/numerical/AverageVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/CoeffVariationVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/CountVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/ExtremeVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/IndicatorVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/MedianVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/RollingKthAverageVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/RollingKthVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/StdevVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/SumVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/TrimmedMeanVisitor.hpp
- interfaces/general-headers/algorithm/visitors/numerical/VarianceVisitor.hpp
- interfaces/general-headers/algorithm/visitors/other/EchoVisitor.hpp
- interfaces/general-headers/algorithm/visitors/other/MultiVisitor.hpp
- interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp
- interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp
- interfaces/general-headers/data/bed/Bed.hpp
- interfaces/general-headers/data/bed/BedCheckIterator.hpp
- interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp
- interfaces/general-headers/data/bed/BedCompare.hpp
- interfaces/general-headers/data/bed/BedDistances.hpp
- interfaces/general-headers/data/bed/BedTypes.hpp
- interfaces/general-headers/data/bed/Bed_minmem.hpp
- interfaces/general-headers/data/measurement/NaN.hpp
- interfaces/general-headers/data/measurement/SelectMeasureType.hpp
- interfaces/general-headers/data/starch/starchApi.hpp
- interfaces/general-headers/data/starch/starchBase64Coding.h
- interfaces/general-headers/data/starch/starchConstants.h
- interfaces/general-headers/data/starch/starchFileHelpers.h
- interfaces/general-headers/data/starch/starchHelpers.h
- interfaces/general-headers/data/starch/starchMetadataHelpers.h
- interfaces/general-headers/data/starch/unstarchHelpers.h
- interfaces/general-headers/suite/BEDOPS.Constants.hpp
- interfaces/general-headers/suite/BEDOPS.Version.hpp
- interfaces/general-headers/utility/AllocateIterator.hpp
- interfaces/general-headers/utility/Assertion.hpp
- interfaces/general-headers/utility/BitMonitor.hpp
- interfaces/general-headers/utility/ByLine.hpp
- interfaces/general-headers/utility/CompilerMath.hpp
- interfaces/general-headers/utility/Exception.hpp
- interfaces/general-headers/utility/FPWrap.hpp
- interfaces/general-headers/utility/Factory.hpp
- interfaces/general-headers/utility/Formats.hpp
- interfaces/general-headers/utility/IteratorPair.hpp
- interfaces/general-headers/utility/OrderCompare.hpp
- interfaces/general-headers/utility/PooledMemory.hpp
- interfaces/general-headers/utility/PrintTypes.hpp
- interfaces/general-headers/utility/SingletonType.hpp
- interfaces/general-headers/utility/Typify.hpp
- interfaces/src/algorithm/sweep/WindowSweepImpl.cpp
- interfaces/src/algorithm/sweep/WindowSweepImpl.specialize.cpp
- interfaces/src/data/measurement/NaN.cpp
- interfaces/src/data/starch/starchBase64Coding.c
- interfaces/src/data/starch/starchConstants.c
- interfaces/src/data/starch/starchFileHelpers.c
- interfaces/src/data/starch/starchHelpers.c
- interfaces/src/data/starch/starchMetadataHelpers.c
- interfaces/src/data/starch/unstarchHelpers.c
- packaging/deb/Dockerfile
- packaging/deb/control
- packaging/os_x/BEDOPS.pkgproj
- packaging/rpm/Dockerfile
- packaging/rpm/bedops.spec
- system.mk/Makefile.darwin
- system.mk/Makefile.linux

The diff was not included because it is too large.

View it on GitLab: https://salsa.debian.org/med-team/bedops/-/commit/d714ec38a548ee3138e43627fbe73bf5a5cb7a53

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