Steffen Möller pushed to branch master at Debian Med / bedops
Commits: dd89af26 by Steffen Moeller at 2025-08-18T00:04:42+02:00 New upstream version - - - - - d714ec38 by Steffen Moeller at 2025-08-18T00:04:43+02:00 New upstream version 2.4.42+dfsg - - - - - 6d494c53 by Steffen Moeller at 2025-08-18T00:04:50+02:00 Update upstream source from tag 'upstream/2.4.42+dfsg' Update to upstream version '2.4.42+dfsg' with Debian dir 296ab747d691cd29fc05293b237344621702897e - - - - - 150cb9b7 by Steffen Moeller at 2025-08-18T00:04:51+02:00 Standards-Version: 4.7.2 (routine-update) - - - - - 61a03434 by Steffen Moeller at 2025-08-18T00:28:56+02:00 Adjusted patches to new upstream version. - - - - - 143 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 - debian/changelog - debian/control - debian/patches/2to3.patch - debian/patches/use_debian_libs - 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/-/compare/f595fe92084cd49ee8fce57fd8ecddcb7ac851e8...61a03434afc8ad63f616e0710742b1f49b98eb85 -- View it on GitLab: https://salsa.debian.org/med-team/bedops/-/compare/f595fe92084cd49ee8fce57fd8ecddcb7ac851e8...61a03434afc8ad63f616e0710742b1f49b98eb85 You're receiving this email because of your account on salsa.debian.org.
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