[med-svn] [bedtools] branch debian/unstable updated (9213f1b -> e378656)
Charles Plessy
plessy at moszumanska.debian.org
Fri Sep 4 14:37:09 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository bedtools.
from 9213f1b Fix MIPS build issue
adds 69ca7e9 Changed vector copies to references
adds cd012c6 Completed #181, GFF can have extra fields. Also, SVlen in VCF takes max of more than two numbers (as opposed to min)
adds 76abaf8 formatting
adds b3504ce typo
adds ec74574 Merge remote-tracking branch 'upstream/master'
adds 8b8a9cd Added distinct_sort_num option to VectorOps for groupBy.
adds bb13971 Added distinct_sort_num and distinct_sort_num desc to VectorOps (and groupBy) and KeyListOps. Added -delim to groupBy.
adds 45321a4 Did #147: don't print usage on errors.
adds 107f803 Added -mean to coverage w/ unit test
adds 0c046ca Fixed Bug 254: stranded merge of BedPlus records w/ strand. Added strand to default output for stranded merge. Added and updated unit tests.
adds 16d4db0 Missing file bug223_d.vcf for intersect unit test
adds e1993b5 Merge pull request #247 from nkindlon/master
adds 598edfc Update README.md
adds aa11ef9 Update README.md
adds 8581890 Converted complement to PFM with merge-based approach, sorted input enforced
adds b6f8ff7 Fixed 44: race condition in bgzip for vcf files.
adds f5927cf Fixed bug262: stranded map with BedPlus
adds b0bc5b7 Merge pull request #261 from nkindlon/master
adds d28d1fc 1st check-in: Converted groupby to PFM
adds 53ecd3c New unit tests (with bug fixes) for groupby
adds b1e3d8d Merge pull request #265 from nkindlon/master
adds af0f9fb adds CPPFLAGS to all compilation targets
adds 833bd23 Merge branch 'master' into wip-issue-206
adds 2d7b550 resolve conflict
adds 86bce5c t push origin masterMerge branch 'wookietreiber-wip-issue-206'
adds b47dbef settle on uint32_t signature for QuickString. Resolves #267 and #271?
adds c730e8e [BUG] fix longstanding bug where genomecov did not report chromosomes with no data at all.
adds 5763783 Test compatibility with OS X improved
adds 6debe57 OS X compatibility fix
adds f678c7f Delete temporary files after test completion
adds 462318f Merge pull request #249 from gtamazian/test-fixes
adds b588bec Merge branch 'master' of https://github.com/arq5x/bedtools2
adds eb03af1 add vcfsort script
adds e542de7 add support for -F and -e
adds 602d650 missing genomecov test files
adds 53f7131 coverage does not need op columns. fixes #287
adds e0e4e5d pretty split tests
adds e4908d6 missing doc images. fixes #285
adds 57929b9 add new tests for -e anf -F options
adds e5f7593 update docs for -e and -F
adds 4cba483 update history for 2.25.0
adds e1062a3 update docs version
adds 6ceaef3 Setting Release-Version v2.25.0
adds 2bbd748 docs formatting
adds 9fb71b2 fix Makefile
adds 1d7b0cd Setting Release-Version v2.25.0
new e378656 Merge tag 'v2.25.0' into debian/unstable
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:
Makefile | 10 +-
README.md | 2 +-
docs/conf.py | 4 +-
docs/content/history.rst | 20 +-
docs/content/images/tool-glyphs/random-glyph.ai | 6467 ++++++++++++++++++++
docs/content/images/tool-glyphs/random-glyph.png | Bin 0 -> 30097 bytes
docs/content/tools/coverage.rst | 2 +
docs/content/tools/intersect.rst | 3 +
docs/content/tools/jaccard.rst | 7 +-
docs/content/tools/map.rst | 6 +-
docs/content/tools/subtract.rst | 6 +-
scripts/vcfsort.sh | 13 +
src/annotateBed/Makefile | 2 +-
src/bamToBed/Makefile | 2 +-
src/bamToFastq/Makefile | 2 +-
src/bed12ToBed6/Makefile | 2 +-
src/bedToBam/Makefile | 2 +-
src/bedToIgv/Makefile | 2 +-
src/bedpeToBam/Makefile | 2 +-
src/bedtools.cpp | 13 +-
src/closestFile/Makefile | 2 +-
src/clusterBed/Makefile | 2 +-
src/complementBed/Makefile | 38 -
src/complementBed/complementBed.cpp | 84 -
src/complementBed/complementBed.h | 47 -
src/complementBed/complementMain.cpp | 114 -
src/{subtractFile => complementFile}/Makefile | 9 +-
src/complementFile/complementFile.cpp | 127 +
src/complementFile/complementFile.h | 54 +
src/complementFile/complementHelp.cpp | 36 +
src/coverageFile/coverageFile.cpp | 43 +-
src/coverageFile/coverageFile.h | 1 +
src/coverageFile/coverageHelp.cpp | 2 +
src/expand/Makefile | 2 +-
src/fastaFromBed/Makefile | 2 +-
src/fisher/Makefile | 2 +-
src/flankBed/Makefile | 2 +-
src/genomeCoverageBed/Makefile | 2 +-
src/genomeCoverageBed/genomeCoverageBed.cpp | 55 +-
src/genomeCoverageBed/genomeCoverageBed.h | 8 +-
src/getOverlap/Makefile | 2 +-
src/groupBy/Makefile | 38 +-
src/groupBy/groupBy.cpp | 728 +--
src/groupBy/groupBy.h | 41 +
src/groupBy/groupByHelp.cpp | 92 +
src/intersectFile/Makefile | 2 +-
src/jaccard/Makefile | 2 +-
src/linksBed/Makefile | 2 +-
src/mapFile/Makefile | 2 +-
src/maskFastaFromBed/Makefile | 2 +-
src/mergeFile/Makefile | 2 +-
src/multiBamCov/Makefile | 2 +-
src/multiIntersectBed/Makefile | 2 +-
src/nekSandbox1/Makefile | 2 +-
src/nucBed/Makefile | 2 +-
src/pairToBed/Makefile | 2 +-
src/pairToPair/Makefile | 2 +-
src/randomBed/Makefile | 2 +-
src/regressTest/Makefile | 6 +-
src/reldist/Makefile | 2 +-
src/sampleFile/Makefile | 2 +-
src/shuffleBed/Makefile | 2 +-
src/slopBed/Makefile | 2 +-
src/sortBed/Makefile | 2 +-
src/sortBed/sortBed.cpp | 24 +-
src/spacingFile/Makefile | 2 +-
src/spacingFile/spacingFile.cpp | 5 +-
src/split/Makefile | 2 +-
src/subtractFile/subtractFile.cpp | 2 +-
src/tagBam/Makefile | 2 +-
src/unionBedGraphs/Makefile | 2 +-
src/utils/BamTools-Ancillary/Makefile | 2 +-
src/utils/BamTools/Makefile | 2 +-
src/utils/BinTree/BinTree.cpp | 12 +-
src/utils/BinTree/Makefile | 2 +-
src/utils/BlockedIntervals/Makefile | 2 +-
src/utils/Contexts/ContextBase.cpp | 30 +-
src/utils/Contexts/ContextBase.h | 18 +-
src/utils/Contexts/ContextClosest.cpp | 11 -
src/utils/Contexts/ContextComplement.cpp | 31 +
src/utils/Contexts/ContextComplement.h | 24 +
src/utils/Contexts/ContextCoverage.cpp | 18 +-
src/utils/Contexts/ContextCoverage.h | 4 +-
src/utils/Contexts/ContextGroupBy.cpp | 138 +
src/utils/Contexts/ContextGroupBy.h | 40 +
src/utils/Contexts/ContextIntersect.cpp | 48 +-
src/utils/Contexts/ContextIntersect.h | 23 +-
src/utils/Contexts/Makefile | 13 +-
src/utils/Fasta/Makefile | 2 +-
.../FileReaders/BufferedStreamMgr.cpp | 2 +-
.../FileReaders/BufferedStreamMgr.h | 2 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 5 +-
src/utils/FileRecordTools/FileReaders/Makefile | 2 +-
.../FileReaders/{Makefile => Makefile~} | 8 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 13 +-
.../FileReaders/SingleLineDelimTextFileReader.h | 3 +-
src/utils/FileRecordTools/FileRecordMgr.cpp | 26 +-
src/utils/FileRecordTools/FileRecordMgr.h | 6 +-
src/utils/FileRecordTools/Makefile | 4 +-
src/utils/FileRecordTools/Records/Bed3Interval.h | 2 +-
.../FileRecordTools/Records/BedPlusInterval.cpp | 117 +-
.../FileRecordTools/Records/BedPlusInterval.h | 24 +-
.../FileRecordTools/Records/GffPlusRecord.cpp | 70 +
.../{BedGraphInterval.h => GffPlusRecord.h} | 33 +-
src/utils/FileRecordTools/Records/GffRecord.cpp | 8 +-
src/utils/FileRecordTools/Records/GffRecord.h | 7 +-
src/utils/FileRecordTools/Records/Makefile | 21 +-
.../FileRecordTools/Records/NoPosPlusRecord.cpp | 42 +
.../FileRecordTools/Records/NoPosPlusRecord.h | 41 +
src/utils/FileRecordTools/Records/PlusFields.cpp | 40 +
src/utils/FileRecordTools/Records/PlusFields.h | 39 +
src/utils/FileRecordTools/Records/Record.cpp | 61 +-
src/utils/FileRecordTools/Records/Record.h | 14 +-
src/utils/FileRecordTools/Records/RecordMgr.cpp | 50 +-
src/utils/FileRecordTools/Records/RecordMgr.h | 2 +
src/utils/FileRecordTools/Records/VcfRecord.cpp | 39 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 8 +-
src/utils/GenomeFile/Makefile | 4 +-
src/utils/GenomeFile/NewGenomeFile.cpp | 12 +
src/utils/GenomeFile/NewGenomeFile.h | 2 +
src/utils/KeyListOps/KeyListOps.cpp | 14 +
src/utils/KeyListOps/KeyListOps.h | 2 +-
src/utils/KeyListOps/KeyListOpsMethods.cpp | 19 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 7 +-
src/utils/KeyListOps/Makefile | 2 +-
src/utils/NewChromsweep/Makefile | 2 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 15 +-
src/utils/RecordOutputMgr/Makefile | 2 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 26 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 5 +-
src/utils/VectorOps/Makefile | 2 +-
src/utils/VectorOps/VectorOps.cpp | 33 +-
src/utils/VectorOps/VectorOps.h | 6 +-
src/utils/bedFile/Makefile | 2 +-
src/utils/bedFilePE/Makefile | 2 +-
src/utils/bedGraphFile/Makefile | 2 +-
src/utils/chromsweep/Makefile | 2 +-
src/utils/{aux => driver}/BedtoolsDriver.cpp | 16 +-
src/utils/{aux => driver}/BedtoolsDriver.h | 2 +
src/utils/{aux => driver}/Makefile | 2 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 61 +-
src/utils/fileType/FileRecordTypeChecker.h | 10 +-
src/utils/fileType/Makefile | 2 +-
src/utils/general/CommonHelp.cpp | 11 +-
src/utils/general/Makefile | 4 +-
src/utils/general/QuickString.cpp | 39 +-
src/utils/general/QuickString.h | 7 +-
src/utils/general/Tokenizer.cpp | 4 +-
src/utils/general/Tokenizer.h | 2 +-
src/utils/gzstream/Makefile | 2 +-
src/utils/sequenceUtilities/Makefile | 2 +-
src/utils/tabFile/Makefile | 2 +-
src/utils/version/Makefile | 2 +-
src/utils/version/version_release.txt | 6 +-
src/windowBed/Makefile | 2 +-
src/windowMaker/Makefile | 2 +-
test/coverage/test-coverage.sh | 587 +-
test/general/test-general.sh | 2 +-
test/genomecov/test-genomecov.sh | 92 +-
test/genomecov/y.bam | Bin 0 -> 220 bytes
test/genomecov/y.bed | 2 +
test/{intersect => groupBy}/a_vcfSVtest.vcf | 0
test/{intersect => groupBy}/gdc.bam | Bin
test/groupBy/noPosvalues.header.bed | 13 +
test/groupBy/test-groupby.sh | 339 +-
test/groupBy/values3.7fields.header.bed | 13 +
.../values3.bed => groupBy/values3.no_header.bed} | 0
.../values3.unmarked_header.bed} | 1 +
test/groupBy/values3_case.header.bed | 13 +
test/intersect/b.bed | 2 +-
.../intersect/bug223_d.vcf | 0
test/intersect/bug44_a.vcf.gz | Bin 0 -> 32419 bytes
test/intersect/bug44_b.bed | 19 +
test/intersect/e.bed | 1 +
test/intersect/foo | 1 +
.../multi_intersect/test-multi_intersect.sh | 2 +-
test/intersect/new_test-intersect.sh | 7 +-
test/intersect/{bug223_sv1_b.vcf => svlen.vcf} | 1 +
test/intersect/test-intersect.sh | 148 +-
test/intersect/two_blocks_partial.bam.bai | Bin 0 -> 832 bytes
test/intersect/x.bam | Bin 0 -> 1755 bytes
test/intersect/x.bed | 3 +
test/intersect/y.bed | 2 +
test/map/bug262_a.bed | 2 +
test/map/bug262_b.bed | 2 +
test/map/test-map.sh | 29 +
test/merge/bug254_c.bed | 4 +
test/merge/bug254_d.bed | 4 +
test/merge/bug254_e.bed | 4 +
test/merge/test-merge.sh | 31 +-
test/sample/test-sample.sh | 1 +
test/sort/a.bed | 11 +
test/sort/names.txt | 3 +
test/sort/test-sort.sh | 176 +
test/split/test-split.sh | 59 +-
test/test.sh | 3 +
196 files changed, 9525 insertions(+), 1681 deletions(-)
create mode 100644 docs/content/images/tool-glyphs/random-glyph.ai
create mode 100644 docs/content/images/tool-glyphs/random-glyph.png
create mode 100755 scripts/vcfsort.sh
delete mode 100644 src/complementBed/Makefile
delete mode 100644 src/complementBed/complementBed.cpp
delete mode 100644 src/complementBed/complementBed.h
delete mode 100644 src/complementBed/complementMain.cpp
copy src/{subtractFile => complementFile}/Makefile (86%)
create mode 100644 src/complementFile/complementFile.cpp
create mode 100644 src/complementFile/complementFile.h
create mode 100644 src/complementFile/complementHelp.cpp
create mode 100644 src/groupBy/groupBy.h
create mode 100644 src/groupBy/groupByHelp.cpp
create mode 100644 src/utils/Contexts/ContextComplement.cpp
create mode 100644 src/utils/Contexts/ContextComplement.h
create mode 100644 src/utils/Contexts/ContextGroupBy.cpp
create mode 100644 src/utils/Contexts/ContextGroupBy.h
copy src/utils/FileRecordTools/FileReaders/{Makefile => Makefile~} (73%)
create mode 100644 src/utils/FileRecordTools/Records/GffPlusRecord.cpp
copy src/utils/FileRecordTools/Records/{BedGraphInterval.h => GffPlusRecord.h} (50%)
create mode 100644 src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp
create mode 100644 src/utils/FileRecordTools/Records/NoPosPlusRecord.h
create mode 100644 src/utils/FileRecordTools/Records/PlusFields.cpp
create mode 100644 src/utils/FileRecordTools/Records/PlusFields.h
rename src/utils/{aux => driver}/BedtoolsDriver.cpp (87%)
rename src/utils/{aux => driver}/BedtoolsDriver.h (84%)
rename src/utils/{aux => driver}/Makefile (98%)
create mode 100644 test/genomecov/y.bam
create mode 100644 test/genomecov/y.bed
copy test/{intersect => groupBy}/a_vcfSVtest.vcf (100%)
copy test/{intersect => groupBy}/gdc.bam (100%)
create mode 100644 test/groupBy/noPosvalues.header.bed
create mode 100644 test/groupBy/values3.7fields.header.bed
copy test/{map/values3.bed => groupBy/values3.no_header.bed} (100%)
copy test/{map/values3.bed => groupBy/values3.unmarked_header.bed} (91%)
create mode 100644 test/groupBy/values3_case.header.bed
copy {debian/test_missing_files => test}/intersect/bug223_d.vcf (100%)
create mode 100644 test/intersect/bug44_a.vcf.gz
create mode 100644 test/intersect/bug44_b.bed
create mode 100644 test/intersect/e.bed
create mode 100644 test/intersect/foo
copy test/intersect/{bug223_sv1_b.vcf => svlen.vcf} (67%)
create mode 100644 test/intersect/two_blocks_partial.bam.bai
create mode 100644 test/intersect/x.bam
create mode 100644 test/intersect/x.bed
create mode 100644 test/intersect/y.bed
create mode 100644 test/map/bug262_a.bed
create mode 100644 test/map/bug262_b.bed
create mode 100644 test/merge/bug254_c.bed
create mode 100644 test/merge/bug254_d.bed
create mode 100644 test/merge/bug254_e.bed
create mode 100644 test/sort/a.bed
create mode 100644 test/sort/names.txt
create mode 100644 test/sort/test-sort.sh
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