Package: bedtools | Debian Sources

Package: bedtools / 2.26.0+dfsg-3

Metadata

Package	Version	Patches format
bedtools	2.26.0+dfsg-3	3.0 (quilt)

Patch series

view the series file

Patch	File delta	Description
gzstream.h.patch \| (download)	src/utils/gzstream/gzstream.C \| 2 1 + 1 - 0 ! 1 file changed, 1 insertion(+), 1 deletion(-)	to find gzstream.h during debian package building.
fix_test_script.patch \| (download)	test/merge/test-merge.sh \| 2 1 + 1 - 0 ! 1 file changed, 1 insertion(+), 1 deletion(-)	use environment variable to find bedtools in all cases
remove_barski_binding_site.png.patch \| (download)	docs/content/tools/genomecov.rst \| 7 2 + 5 - 0 ! 1 file changed, 2 insertions(+), 5 deletions(-)	---
reproducible_build.patch \| (download)	Makefile \| 2 1 + 1 - 0 ! 1 file changed, 1 insertion(+), 1 deletion(-)	enable reproducible builds
v2.26.0 19 g6bf23c4.patch \| (download)	Makefile \| 2 1 + 1 - 0 ! docs/content/history.rst \| 33 17 + 16 - 0 ! docs/index.rst \| 1 1 + 0 - 0 ! docs/templates/sidebar-intro.html \| 2 1 + 1 - 0 ! src/bedtools.cpp \| 17 11 + 6 - 0 ! src/complementFile/complementFile.cpp \| 18 9 + 9 - 0 ! src/complementFile/complementFile.h \| 6 3 + 3 - 0 ! src/coverageFile/coverageFile.cpp \| 219 132 + 87 - 0 ! src/coverageFile/coverageFile.h \| 7 3 + 4 - 0 ! src/fisher/fisher.cpp \| 4 2 + 2 - 0 ! src/groupBy/Makefile \| 1 1 + 0 - 0 ! src/groupBy/groupBy.cpp \| 72 45 + 27 - 0 ! src/groupBy/groupBy.h \| 8 4 + 4 - 0 ! src/intersectFile/intersectFile.cpp \| 14 6 + 8 - 0 ! src/intersectFile/intersectFile.h \| 8 4 + 4 - 0 ! src/jaccard/jaccard.cpp \| 6 3 + 3 - 0 ! src/jaccard/jaccard.h \| 8 4 + 4 - 0 ! src/nekSandbox1/nekSandboxMain.cpp \| 14 7 + 7 - 0 ! src/regressTest/regressTestMain.cpp \| 4 2 + 2 - 0 ! src/shiftBed/shiftBed.cpp \| 4 2 + 2 - 0 ! src/shuffleBed/shuffleBed.cpp \| 54 17 + 37 - 0 ! src/spacingFile/spacingFile.cpp \| 9 7 + 2 - 0 ! src/spacingFile/spacingFile.h \| 8 4 + 4 - 0 ! src/subtractFile/subtractFile.cpp \| 6 3 + 3 - 0 ! src/utils/BinTree/BinTree.cpp \| 20 10 + 10 - 0 ! src/utils/BinTree/BinTree.h \| 10 5 + 5 - 0 ! src/utils/Contexts/ContextBase.cpp \| 25 12 + 13 - 0 ! src/utils/Contexts/ContextBase.h \| 42 21 + 21 - 0 ! src/utils/Contexts/ContextClosest.cpp \| 6 3 + 3 - 0 ! src/utils/Contexts/ContextGroupBy.cpp \| 10 6 + 4 - 0 ! src/utils/Contexts/ContextGroupBy.h \| 8 4 + 4 - 0 ! src/utils/Contexts/ContextIntersect.h \| 8 4 + 4 - 0 ! src/utils/Contexts/Makefile \| 2 1 + 1 - 0 ! src/utils/FileRecordTools/FileReaders/BamFileReader.cpp \| 8 4 + 4 - 0 ! src/utils/FileRecordTools/FileReaders/BamFileReader.h \| 14 7 + 7 - 0 ! src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp \| 4 2 + 2 - 0 ! src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h \| 10 5 + 5 - 0 ! src/utils/FileRecordTools/FileReaders/FileReader.h \| 4 2 + 2 - 0 ! src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp \| 10 4 + 6 - 0 ! src/utils/FileRecordTools/FileReaders/InputStreamMgr.h \| 12 6 + 6 - 0 ! src/utils/FileRecordTools/FileReaders/Makefile \| 8 4 + 4 - 0 ! src/utils/FileRecordTools/FileReaders/Makefile~ \| 2 1 + 1 - 0 ! src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp \| 22 12 + 10 - 0 ! src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h \| 18 9 + 9 - 0 ! src/utils/FileRecordTools/FileRecordMergeMgr.cpp \| 8 4 + 4 - 0 ! src/utils/FileRecordTools/FileRecordMergeMgr.h \| 2 1 + 1 - 0 ! src/utils/FileRecordTools/FileRecordMgr.cpp \| 21 8 + 13 - 0 ! src/utils/FileRecordTools/FileRecordMgr.h \| 14 7 + 7 - 0 ! src/utils/FileRecordTools/Makefile \| 18 9 + 9 - 0 ! src/utils/FileRecordTools/Records/BamRecord.cpp \| 112 60 + 52 - 0 ! src/utils/FileRecordTools/Records/BamRecord.h \| 30 15 + 15 - 0 ! src/utils/FileRecordTools/Records/Bed12Interval.cpp \| 48 24 + 24 - 0 ! src/utils/FileRecordTools/Records/Bed12Interval.h \| 31 14 + 17 - 0 ! src/utils/FileRecordTools/Records/Bed3Interval.cpp \| 38 21 + 17 - 0 ! src/utils/FileRecordTools/Records/Bed3Interval.h \| 12 6 + 6 - 0 ! src/utils/FileRecordTools/Records/Bed4Interval.cpp \| 18 9 + 9 - 0 ! src/utils/FileRecordTools/Records/Bed4Interval.h \| 10 5 + 5 - 0 ! src/utils/FileRecordTools/Records/Bed5Interval.cpp \| 22 11 + 11 - 0 ! src/utils/FileRecordTools/Records/Bed5Interval.h \| 10 5 + 5 - 0 ! src/utils/FileRecordTools/Records/Bed6Interval.cpp \| 28 14 + 14 - 0 ! src/utils/FileRecordTools/Records/Bed6Interval.h \| 10 5 + 5 - 0 ! src/utils/FileRecordTools/Records/BedGraphInterval.cpp \| 16 8 + 8 - 0 ! src/utils/FileRecordTools/Records/BedGraphInterval.h \| 10 5 + 5 - 0 ! src/utils/FileRecordTools/Records/BedPlusInterval.cpp \| 24 13 + 11 - 0 ! src/utils/FileRecordTools/Records/BedPlusInterval.h \| 14 7 + 7 - 0 ! src/utils/FileRecordTools/Records/BlockMgr.cpp \| 103 60 + 43 - 0 ! src/utils/FileRecordTools/Records/BlockMgr.h \| 8 5 + 3 - 0 ! src/utils/FileRecordTools/Records/GffPlusRecord.cpp \| 10 5 + 5 - 0 ! src/utils/FileRecordTools/Records/GffPlusRecord.h \| 10 5 + 5 - 0 ! src/utils/FileRecordTools/Records/GffRecord.cpp \| 74 38 + 36 - 0 ! src/utils/FileRecordTools/Records/GffRecord.h \| 24 12 + 12 - 0 ! src/utils/FileRecordTools/Records/Makefile \| 18 9 + 9 - 0 ! src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp \| 4 2 + 2 - 0 ! src/utils/FileRecordTools/Records/NoPosPlusRecord.h \| 4 2 + 2 - 0 ! src/utils/FileRecordTools/Records/PlusFields.cpp \| 7 3 + 4 - 0 ! src/utils/FileRecordTools/Records/PlusFields.h \| 9 5 + 4 - 0 ! src/utils/FileRecordTools/Records/Record.cpp \| 28 21 + 7 - 0 ! src/utils/FileRecordTools/Records/Record.h \| 65 36 + 29 - 0 ! src/utils/FileRecordTools/Records/RecordKeyList.cpp \| 8 4 + 4 - 0 ! src/utils/FileRecordTools/Records/RecordKeyList.h \| 6 3 + 3 - 0 ! src/utils/FileRecordTools/Records/RecordKeyVector.cpp \| 28 20 + 8 - 0 ! src/utils/FileRecordTools/Records/RecordKeyVector.h \| 15 8 + 7 - 0 ! src/utils/FileRecordTools/Records/RecordList.cpp \| 5 3 + 2 - 0 ! src/utils/FileRecordTools/Records/RecordList.h \| 12 6 + 6 - 0 ! src/utils/FileRecordTools/Records/VcfRecord.cpp \| 33 17 + 16 - 0 ! src/utils/FileRecordTools/Records/VcfRecord.h \| 16 8 + 8 - 0 ! src/utils/GenomeFile/NewGenomeFile.cpp \| 12 6 + 6 - 0 ! src/utils/GenomeFile/NewGenomeFile.h \| 24 12 + 12 - 0 ! src/utils/KeyListOps/KeyListOps.cpp \| 80 41 + 39 - 0 ! src/utils/KeyListOps/KeyListOps.h \| 38 19 + 19 - 0 ! src/utils/KeyListOps/KeyListOpsMethods.cpp \| 69 39 + 30 - 0 ! src/utils/KeyListOps/KeyListOpsMethods.h \| 54 27 + 27 - 0 ! src/utils/NewChromsweep/CloseSweep.cpp \| 22 11 + 11 - 0 ! src/utils/NewChromsweep/CloseSweep.h \| 22 11 + 11 - 0 ! src/utils/NewChromsweep/NewChromsweep.cpp \| 57 33 + 24 - 0 ! src/utils/NewChromsweep/NewChromsweep.h \| 18 9 + 9 - 0 ! src/utils/RecordOutputMgr/RecordOutputMgr.cpp \| 54 33 + 21 - 0 ! src/utils/RecordOutputMgr/RecordOutputMgr.h \| 14 7 + 7 - 0 ! src/utils/bedFile/bedFile.cpp \| 37 36 + 1 - 0 ! src/utils/bedFile/bedFile.h \| 23 17 + 6 - 0 ! src/utils/driver/BedtoolsDriver.cpp \| 2 1 + 1 - 0 ! src/utils/driver/BedtoolsDriver.h \| 6 3 + 3 - 0 ! src/utils/fileType/FileRecordTypeChecker.cpp \| 8 4 + 4 - 0 ! src/utils/fileType/FileRecordTypeChecker.h \| 4 2 + 2 - 0 ! src/utils/fileType/Makefile \| 2 1 + 1 - 0 ! src/utils/general/BTlist.h \| 16 9 + 7 - 0 ! src/utils/general/BedtoolsTypes.h \| 2 1 + 1 - 0 ! src/utils/general/Makefile \| 6 3 + 3 - 0 ! src/utils/general/ParseTools.cpp \| 18 13 + 5 - 0 ! src/utils/general/ParseTools.h \| 14 7 + 7 - 0 ! src/utils/general/QuickString.cpp \| 96 48 + 48 - 0 ! src/utils/general/QuickString.h \| 78 39 + 39 - 0 ! src/utils/general/Tokenizer.cpp \| 9 5 + 4 - 0 ! src/utils/general/Tokenizer.h \| 4 2 + 2 - 0 ! src/utils/stringUtilities/stringUtilities.h \| 18 16 + 2 - 0 ! test/coverage/test-coverage.sh \| 2 1 + 1 - 0 ! test/general/t.bed \| 5 5 + 0 - 0 ! test/general/test-general.sh \| 11 11 + 0 - 0 ! test/groupBy/test-groupby.sh \| 5 2 + 3 - 0 ! test/shift/b.bed \| 2 2 + 0 - 0 ! test/shift/huge.genome \| 1 1 + 0 - 0 ! test/shift/test-shift.sh \| 11 11 + 0 - 0 ! test/test.sh \| 3 3 + 0 - 0 ! 123 files changed, 1425 insertions(+), 1173 deletions(-)	sync with upstream repo at commit 6bf23c This patch contains bug fixes to upstream issues #429, #418 and #424. In particular, it repairs the groupby command, which was completely broken. Cherry-picking a single commit did not result in a buildable source, and this big patch was the easiest alternative.

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