[med-svn] [bedtools] branch master updated (4272686 -> cbb3284)
Andreas Tille
tille at debian.org
Sat Feb 10 08:58:02 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository bedtools.
from 4272686 bedtools (2.26.0+dfsg-5) UNRELEASED;unstable; urgency=medium
new c6cc550 New upstream version 2.27.1+dfsg
new 1ee79d3 Update upstream source from tag '2.27.1+dfsg'
new 9572611 New upstream version
new b98c017 Refresh patches
new cbb3284 Remove patch which now rather leads to failure of test
The 5 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 +-
debian/changelog | 6 +
.../do_not_let_random_failure_tests_fail.patch | 3 +
debian/patches/fix_test_script.patch | 2 +-
debian/patches/reproducible_build.patch | 2 +-
debian/patches/series | 2 +-
debian/patches/v2.26.0-19-g6bf23c4.patch | 6707 +------------
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 +-
...ew_test-intersect.sh => new_test-intersect.sh~} | 142 +-
.../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 +-
246 files changed, 13628 insertions(+), 9485 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
copy test/intersect/{new_test-intersect.sh => new_test-intersect.sh~} (75%)
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
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