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.