[med-svn] [bedtools] branch upstream updated (f2b5aa1 -> c6cc550)
Andreas Tille
tille at debian.org
Sat Feb 10 08:58:06 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository bedtools.
from f2b5aa1 Imported Upstream version 2.26.0+dfsg
new c6cc550 New upstream version 2.27.1+dfsg
The 1 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:
.travis.yml | 5 +
Makefile | 11 +-
docs/conf.py | 6 +-
docs/content/advanced-usage.rst | 10 +-
docs/content/faq.rst | 7 +
docs/content/general-usage.rst | 2 +
docs/content/history.rst | 52 +-
docs/content/installation.rst | 2 +-
docs/content/tools/bamtobed.rst | 1 +
docs/content/tools/bed12tobed6.rst | 2 +
docs/content/tools/bedtobam.rst | 3 +
docs/content/tools/closest.rst | 2 +-
docs/content/tools/coverage.rst | 2 +-
docs/content/tools/genomecov.rst | 2 +-
docs/content/tools/getfasta.rst | 2 +-
docs/content/tools/intersect.rst | 4 +-
docs/content/tools/links.rst | 4 +
docs/content/tools/overlap.rst | 3 +
docs/content/tools/pairtopair.rst | 4 +
docs/content/tools/sort.rst | 39 +-
docs/content/tools/subtract.rst | 5 +-
docs/content/tools/unionbedg.rst | 1 +
docs/content/tools/window.rst | 4 +-
docs/index.rst | 11 +
docs/templates/sidebar-intro.html | 2 +-
src/annotateBed/annotateBed.cpp | 4 +-
src/bed12ToBed6/bed12ToBed6.cpp | 3 +-
src/bedtools.cpp | 35 +-
src/closestFile/closestHelp.cpp | 2 -
src/clusterBed/clusterBed.h | 1 +
src/clusterBed/clusterMain.cpp | 18 +-
src/complementFile/complementFile.cpp | 18 +-
src/complementFile/complementFile.h | 6 +-
src/complementFile/complementHelp.cpp | 2 -
src/coverageFile/coverageFile.cpp | 183 +-
src/coverageFile/coverageFile.h | 9 +-
src/coverageFile/coverageHelp.cpp | 2 -
src/fastaFromBed/fastaFromBed.cpp | 94 +-
src/fastaFromBed/fastaFromBed.h | 9 +-
src/fastaFromBed/fastaFromBedMain.cpp | 18 +-
src/fisher/fisher.cpp | 17 +-
src/fisher/fisherHelp.cpp | 4 -
src/genomeCoverageBed/genomeCoverageBed.cpp | 2 +-
src/genomeCoverageBed/genomeCoverageMain.cpp | 4 +
src/groupBy/Makefile | 1 +
src/groupBy/groupBy.cpp | 74 +-
src/groupBy/groupBy.h | 10 +-
src/intersectFile/intersectFile.cpp | 15 +-
src/intersectFile/intersectFile.h | 10 +-
src/intersectFile/intersectHelp.cpp | 5 +-
src/jaccard/jaccard.cpp | 6 +-
src/jaccard/jaccard.h | 8 +-
src/jaccard/jaccardHelp.cpp | 4 -
src/mapFile/mapHelp.cpp | 4 -
src/maskFastaFromBed/Makefile | 3 +-
src/maskFastaFromBed/maskFastaFromBed.cpp | 26 +-
src/maskFastaFromBed/maskFastaFromBed.h | 7 +-
src/maskFastaFromBed/maskFastaFromBedMain.cpp | 33 +-
src/mergeFile/mergeHelp.cpp | 4 -
src/multiBamCov/multiBamCov.cpp | 4 +-
src/nekSandbox1/nekSandboxMain.cpp | 14 +-
src/regressTest/regressTestMain.cpp | 4 +-
src/reldist/reldist.cpp | 12 +-
src/sampleFile/sampleHelp.cpp | 5 -
src/shiftBed/shiftBed.cpp | 6 +-
src/shuffleBed/shuffleBed.cpp | 102 +-
src/shuffleBed/shuffleBed.h | 6 +
src/slopBed/slopBed.cpp | 65 +-
src/sortBed/sortBed.h | 1 +
src/sortBed/sortMain.cpp | 27 +-
src/spacingFile/spacingFile.cpp | 9 +-
src/spacingFile/spacingFile.h | 8 +-
src/spacingFile/spacingHelp.cpp | 12 +-
src/subtractFile/subtractFile.cpp | 14 +-
src/subtractFile/subtractHelp.cpp | 4 -
src/utils/BamTools/src/api/BamConstants.h | 6 +-
.../src/api/internal/bam/BamMultiReader_p.cpp | 4 +-
.../BamTools/src/api/internal/io/HostAddress_p.cpp | 2 +-
src/utils/BinTree/BinTree.cpp | 20 +-
src/utils/BinTree/BinTree.h | 10 +-
src/utils/Contexts/ContextBase.cpp | 45 +-
src/utils/Contexts/ContextBase.h | 44 +-
src/utils/Contexts/ContextClosest.cpp | 6 +-
src/utils/Contexts/ContextGroupBy.cpp | 10 +-
src/utils/Contexts/ContextGroupBy.h | 8 +-
src/utils/Contexts/ContextIntersect.cpp | 9 -
src/utils/Contexts/ContextIntersect.h | 8 +-
src/utils/Contexts/ContextMerge.cpp | 8 +-
src/utils/Contexts/ContextMerge.h | 2 +-
src/utils/Contexts/ContextSubtract.cpp | 19 +-
src/utils/Contexts/ContextSubtract.h | 2 +-
src/utils/Contexts/Makefile | 2 +-
.../FileRecordTools/FileReaders/BamFileReader.cpp | 8 +-
.../FileRecordTools/FileReaders/BamFileReader.h | 14 +-
.../FileReaders/BufferedStreamMgr.cpp | 6 +-
.../FileReaders/BufferedStreamMgr.h | 10 +-
src/utils/FileRecordTools/FileReaders/FileReader.h | 4 +-
.../FileRecordTools/FileReaders/InputStreamMgr.cpp | 10 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 12 +-
src/utils/FileRecordTools/FileReaders/Makefile | 8 +-
src/utils/FileRecordTools/FileReaders/Makefile~ | 2 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 22 +-
.../FileReaders/SingleLineDelimTextFileReader.h | 18 +-
src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 8 +-
src/utils/FileRecordTools/FileRecordMergeMgr.h | 2 +-
src/utils/FileRecordTools/FileRecordMgr.cpp | 34 +-
src/utils/FileRecordTools/FileRecordMgr.h | 18 +-
src/utils/FileRecordTools/Makefile | 18 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 112 +-
src/utils/FileRecordTools/Records/BamRecord.h | 30 +-
.../FileRecordTools/Records/Bed12Interval.cpp | 48 +-
src/utils/FileRecordTools/Records/Bed12Interval.h | 31 +-
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 38 +-
src/utils/FileRecordTools/Records/Bed3Interval.h | 12 +-
src/utils/FileRecordTools/Records/Bed4Interval.cpp | 18 +-
src/utils/FileRecordTools/Records/Bed4Interval.h | 10 +-
src/utils/FileRecordTools/Records/Bed5Interval.cpp | 22 +-
src/utils/FileRecordTools/Records/Bed5Interval.h | 10 +-
src/utils/FileRecordTools/Records/Bed6Interval.cpp | 28 +-
src/utils/FileRecordTools/Records/Bed6Interval.h | 10 +-
.../FileRecordTools/Records/BedGraphInterval.cpp | 16 +-
.../FileRecordTools/Records/BedGraphInterval.h | 10 +-
.../FileRecordTools/Records/BedPlusInterval.cpp | 24 +-
.../FileRecordTools/Records/BedPlusInterval.h | 14 +-
src/utils/FileRecordTools/Records/BlockMgr.cpp | 36 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 9 +-
.../FileRecordTools/Records/GffPlusRecord.cpp | 10 +-
src/utils/FileRecordTools/Records/GffPlusRecord.h | 10 +-
src/utils/FileRecordTools/Records/GffRecord.cpp | 74 +-
src/utils/FileRecordTools/Records/GffRecord.h | 24 +-
src/utils/FileRecordTools/Records/Makefile | 18 +-
.../FileRecordTools/Records/NoPosPlusRecord.cpp | 4 +-
.../FileRecordTools/Records/NoPosPlusRecord.h | 4 +-
src/utils/FileRecordTools/Records/PlusFields.cpp | 7 +-
src/utils/FileRecordTools/Records/PlusFields.h | 9 +-
src/utils/FileRecordTools/Records/Record.cpp | 28 +-
src/utils/FileRecordTools/Records/Record.h | 65 +-
.../FileRecordTools/Records/RecordKeyList.cpp | 8 +-
src/utils/FileRecordTools/Records/RecordKeyList.h | 6 +-
.../FileRecordTools/Records/RecordKeyVector.cpp | 28 +-
.../FileRecordTools/Records/RecordKeyVector.h | 15 +-
src/utils/FileRecordTools/Records/RecordList.cpp | 5 +-
src/utils/FileRecordTools/Records/RecordList.h | 12 +-
src/utils/FileRecordTools/Records/StrandQueue.cpp | 18 +-
src/utils/FileRecordTools/Records/StrandQueue.h | 14 +-
src/utils/FileRecordTools/Records/VcfRecord.cpp | 33 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 16 +-
src/utils/GenomeFile/NewGenomeFile.cpp | 16 +-
src/utils/GenomeFile/NewGenomeFile.h | 24 +-
src/utils/KeyListOps/KeyListOps.cpp | 100 +-
src/utils/KeyListOps/KeyListOps.h | 38 +-
src/utils/KeyListOps/KeyListOpsMethods.cpp | 77 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 54 +-
src/utils/NewChromsweep/CloseSweep.cpp | 177 +-
src/utils/NewChromsweep/CloseSweep.h | 35 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 61 +-
src/utils/NewChromsweep/NewChromsweep.h | 18 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 81 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 14 +-
src/utils/bedFile/bedFile.cpp | 50 +-
src/utils/bedFile/bedFile.h | 23 +-
src/utils/driver/BedtoolsDriver.cpp | 6 +-
src/utils/driver/BedtoolsDriver.h | 9 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 22 +-
src/utils/fileType/FileRecordTypeChecker.h | 6 +-
src/utils/fileType/Makefile | 2 +-
src/utils/general/BTlist.h | 16 +-
src/utils/general/BedtoolsTypes.h | 2 +-
src/utils/general/Makefile | 6 +-
src/utils/general/ParseTools.cpp | 42 +-
src/utils/general/ParseTools.h | 15 +-
src/utils/general/QuickString.cpp | 96 +-
src/utils/general/QuickString.h | 78 +-
src/utils/general/Tokenizer.cpp | 9 +-
src/utils/general/Tokenizer.h | 9 +-
src/utils/stringUtilities/stringUtilities.h | 18 +-
src/utils/version/version_release.txt | 6 +-
src/windowBed/windowMain.cpp | 2 +-
test/bamtobed/test-bamtobed.sh | 35 +-
test/bamtofastq/test-bamtofastq.sh | 7 +-
test/bed12tobed6/test-bed12tobed6.sh | 19 +-
test/closest/kclosest/bug471_a.bed | 5 +
test/closest/kclosest/bug471_b.bed | 9 +
test/closest/kclosest/test-kclosest.sh | 262 +-
test/closest/sortAndNaming/test-sort-and-naming.sh | 71 +-
test/closest/test-closest.sh | 168 +-
test/cluster/test-cluster.sh | 17 +-
test/complement/test-complement.sh | 29 +-
test/coverage/chr_0-100.bed | 2 +
test/coverage/test-coverage.sh | 89 +-
test/expand/test-expand.sh | 17 +-
test/fisher/test-fisher.sh | 19 +-
test/flank/test-flank.sh | 35 +-
test/general/a.chromheader.bed | 2 +
test/{map/t.bed => general/a.trackheader.bed} | 1 +
test/general/hg19.fa.fai | 1 +
test/general/t.bed | 5 +
test/general/test-general.sh | 171 +-
test/genomecov/test-genomecov.sh | 37 +-
test/getfasta/test-getfasta.sh | 78 +-
test/{groupBy => groupby}/a_vcfSVtest.vcf | 0
test/groupby/bug569_problem.txt | 4 +
test/{groupBy => groupby}/gdc.bam | Bin
test/{groupBy => groupby}/noPosvalues.header.bed | 0
test/{groupBy => groupby}/test-groupby.sh | 89 +-
test/groupby/test.bed | 3 +
.../values3.7fields.header.bed | 0
test/{groupBy => groupby}/values3.header.bed | 0
test/{groupBy => groupby}/values3.no_header.bed | 0
.../values3.unmarked_header.bed | 2 +-
.../values3.unmarked_header.bed.2} | 2 +-
test/{groupBy => groupby}/values3_case.header.bed | 0
test/intersect/jim.bed | 1 +
test/intersect/jim.vcf | 3 +
.../multi_intersect/test-multi_intersect.sh | 47 +-
test/intersect/new_test-intersect.sh | 185 +-
test/intersect/new_test-intersect.sh~ | 6 +-
.../sortAndNaming/test-sort-and-naming.sh | 73 +-
test/intersect/test-intersect.sh | 231 +-
test/jaccard/test-jaccard.sh | 31 +-
test/makewindows/test-makewindows.sh | 27 +-
test/map/test-map.sh | 121 +-
test/merge/test-merge.sh | 201 +-
test/multicov/test-multicov.sh | 27 +-
test/negativecontrol/test-negativecontrol.sh | 2 +
test/reldist/test-reldist.sh | 13 +-
test/sample/test-sample.sh | 41 +-
test/shift/b.bed | 2 +
test/shift/huge.genome | 1 +
test/shift/test-shift.sh | 51 +-
test/shuffle/test-shuffle.sh | 145 +-
test/slop/test-slop.sh | 106 +-
test/sort/b.bed | 4 +
test/sort/test-sort.sh | 38 +-
test/spacing/a.bed | 3 +-
test/spacing/test-spacing.sh | 18 +-
test/split/randData.bed | 10000 +++++++++++++++++++
test/split/test-split.sh | 32 +-
test/subtract/test-subtract.sh | 51 +-
test/test.sh | 99 +-
240 files changed, 13580 insertions(+), 2675 deletions(-)
create mode 100644 test/closest/kclosest/bug471_a.bed
create mode 100644 test/closest/kclosest/bug471_b.bed
create mode 100644 test/coverage/chr_0-100.bed
mode change 100644 => 100755 test/coverage/test-coverage.sh
create mode 100644 test/general/a.chromheader.bed
copy test/{map/t.bed => general/a.trackheader.bed} (64%)
create mode 100644 test/general/hg19.fa.fai
create mode 100644 test/general/t.bed
rename test/{groupBy => groupby}/a_vcfSVtest.vcf (100%)
create mode 100644 test/groupby/bug569_problem.txt
rename test/{groupBy => groupby}/gdc.bam (100%)
rename test/{groupBy => groupby}/noPosvalues.header.bed (100%)
rename test/{groupBy => groupby}/test-groupby.sh (83%)
create mode 100644 test/groupby/test.bed
rename test/{groupBy => groupby}/values3.7fields.header.bed (100%)
copy test/{groupBy => groupby}/values3.header.bed (100%)
rename test/{groupBy => groupby}/values3.no_header.bed (100%)
rename test/{groupBy => groupby}/values3.unmarked_header.bed (91%)
rename test/{groupBy/values3.header.bed => groupby/values3.unmarked_header.bed.2} (90%)
rename test/{groupBy => groupby}/values3_case.header.bed (100%)
create mode 100644 test/intersect/jim.bed
create mode 100644 test/intersect/jim.vcf
create mode 100644 test/negativecontrol/test-negativecontrol.sh
create mode 100644 test/shift/b.bed
create mode 100644 test/shift/huge.genome
create mode 100755 test/sort/b.bed
create mode 100644 test/split/randData.bed
mode change 100644 => 100755 test/test.sh
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git
More information about the debian-med-commit
mailing list