[med-svn] [bedtools] branch master updated (9b536ae -> 8e1a406)
Charles Plessy
plessy at moszumanska.debian.org
Thu Jul 7 04:50:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository bedtools.
from 9b536ae Merge branch 'master' of https://github.com/arq5x/bedtools2
new 7c36bfa fix memory leak during sweep's closeOut of DB files.
new 97a2235 Added chrMT, fixed genome name
new 6cca09e LF line endings, 644 file mode genomes
new d2d9c95 Added mm10 chrMT entry
new 0836fed Merge pull request #289 from LukeGoodsell/feature/chrMT
new c99baef Merge branch 'master' of https://github.com/arq5x/bedtools2
new a86243d BAM files, genomecov pair-end fragment size, or fixedFragment size -pc -fs
new 728e07a BUG Fix
new b401c43 Check if right side goes below 0
new a8162a6 Documentation added - corrected binding for start end
new 02e48c2 Merge pull request #318 from SciDAP/master
new 9b34f4b Fixes #334. Remove extraneous tab from BED4::printNull(). Thanks to @dwaggott.
new f91a32d Fixes #329. groupby handles single column input.
new 95655a0 Fixes #321. Enable freqasc and freqdesc in groupby.
new 98b4402 tab delimited mm10
new e4c5e55 update installation instructions to use github.
new d188b65 fix double comparisons to zero
new 5d6f024 Merge branch 'master' of https://github.com/arq5x/bedtools2
new 6d3fcbc fix typo in closest doc glyph
new 78d74e9 -r should force the value for -F for intersect.
new 22f445a Allow for overwriting the prefix
new 8107e8a Merge pull request #345 from bgruening/patch-1
new bb7cbfe Merge branch 'master' of https://github.com/arq5x/bedtools2
new 9b734e6 missing null printing for GffPlusRecords.
new a307830 show help if solely sub-command is given.
new d6e2ae4 restore -grp, -opCols and -ops to groupby. Resolves #300
new 2bbe124 add -bedOut option to getfasta
new 4e1b658 remove -fo from getfasta. always go to stdout.
new fe3bd3f fix null reporting with multiple db files.
new 1ae009d add tests
new 44ca4e9 one too few tabs in annotate -names
new f2f521d #325 allow -s and -w to b used in any order for makewindows
new 6b75c05 add a 'shift' tool
new 1f27837 document shift tool
new 9bab0f9 update authorship
new 91ffc1d test for shifts greater than signed int
new 6d8db56 Add shift tests to test scripts
new de9b06a move shift size calc to AddShift
new f250e10 Merge pull request #350 from davidrichardson/dr_shift
new f09d845 Changed expected output for merge.t11 to reflect the current output of merge. The test now passes.
new 5b590f9 Merge pull request #328 from skotchandsoda/master
new baa5137 Merge branch 'master' of https://github.com/arq5x/bedtools2
new 89cde77 try to fix gcc5+ errors and silence various warnings.
new a3e17ca fix getfasta tests in light of the removal of -fo
new 447c995 fix getfasta tests to account for removal of -fo option
new 401c61d update docs for -dz
new 577fecf fix for issue #356
new af82217 enable stdev and sstdev for groupby. fixes issue #367
new 5e293d4 use STL tokenizer to split on ','. Addresses #366
new a64248d Merge branch 'issue_366'
new d3f4654 add test for issue 366
new b2615f8 Fix KeyListOps stddev and min/max methods
new 5e7c696 Merge pull request #369 from jmarshall/KeyListOps
new 42abf50 cleanup
new 8dfe9b8 complement: check intervals agains chrom len. resolves #376
new f96fcd8 Allow debug builds in Makefile.
new 1305e92 Merge pull request #375 from yesimon/make_debug
new 3508355 add long stuff found by @ryanlayer's compiler settings.
new 9966011 Merge pull request #379 from brentp/fisher-long
new a5ea332 Merge branch 'master' of https://github.com/arq5x/bedtools2
new e9e6b9a shuffle: warn when ivl exceeds max chrom length. Fixes #377
new 25cf6fd Fix complement segfault for empty input intervals.
new fddd08a merge pull #374
new 76b36e2 Merge branch 'yesimon-complementfile_empty'
new 1b2443b Fix typo in docs
new 671d044 Merge pull request #380 from rmzelle/patch-1
new c1dbdd6 Merge branch 'master' of https://github.com/arq5x/bedtools2
new 7b930d9 coverage: correctly compute depth for -split. resolves #354
new b0328c3 update tutorial link.
new 28a2f5c Remove excess const from function return types
new 7c6fdb7 Fix typo [minor]
new 2a99966 Merge pull request #382 from jmarshall/intel-warnings
new 5ee3285 Merge branch 'master' of https://github.com/arq5x/bedtools2
new 78826cb fix the counting of hit distances in closest.
new 2523c35 update tests for closest -mdb based on issue reported by Jo on 11-Apr-2016
new 42b1de1 force makewindows to always create -n windows from a BED record.
new 8435bd3 weighted includes
new fe1eabe Merge pull request #386 from zeeev/master
new 34913f2 Minor typo correction in documentation
new ee72249 Merge pull request #399 from keithcallenberg/patch-1
new 76faa3b Merge branch 'master' of https://github.com/arq5x/bedtools2
new 3d027c9 Addresses #311. fix off by one error when reporting overlaps with VCF or GFF.
new dfff6ba Address #316. Handle both SVLEN and END
new cc3fb42 don't delete testing bams
new fbf2686 resolve further off by one errors when intersecting GFF/VCF and BED
new cf975b2 Merge branch 'issue_311'
new 066075b prevent underflow
new ef73e6e handle multiple, posibble negative SVLENs. choose abs_max.
new 9bfce2d fix map's stdev and sstdev tests
new 3d1831e update general tests
new 780faf7 fix broken SV intersect test
new e51b337 restore -fo option to getfasta for backwards compatibility.
new e88e919 tweak test file.
new 5e87af7 Tip for extracting single region BED files
new e79e3cb Merge pull request #403 from s-boardman/patch-1
new a0dc5db Fixes #407. Force coverage to process every record in query file.
new 5c0e33a first pass
new 17c2172 restore help with -h or --help
new b432a31 cleanup
new 548a3c6 fix for issue #336
new e67accc Added feature: name, chromosome and position in fasta headers #406
new 9e51614 Merge pull request #410 from rishavray/feature/#406getfasta
new 2285e98 add tests for getfasta
new f060164 Fix BedFile::GetNextBed()'s handling of missing newlines
new 5de3a9b Merge pull request #404 from jmarshall/fix-GetNextBed
new c8604e9 update docs for 2.26.0
new b7b2b72 update docs version
new f7d3b7e add -pc to history
new 872220a Setting Release-Version v2.26.0
new 3b91220 cleanup
new a525d82 Setting Release-Version v2.26.0
new e6f27ac missing test files
new 99bead1 missing test files
new 1e16d52 Setting Release-Version v2.26.0
new 8e1a406 Merge branch 'master' of https://github.com/arq5x/bedtools2
The 115 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 | 29 +--
docs/conf.py | 6 +-
docs/content/bedtools-suite.rst | 1 +
docs/content/history.rst | 21 +++
.../images/tool-glyphs/barski_binding_site.png | Bin 0 -> 346688 bytes
docs/content/images/tool-glyphs/closest-glyph.png | Bin 138680 -> 138349 bytes
docs/content/installation.rst | 22 ++-
docs/content/overview.rst | 1 +
docs/content/tools/genomecov.rst | 28 ++-
docs/content/tools/getfasta.rst | 54 ++++--
docs/content/tools/shift.rst | 118 ++++++++++++
docs/index.rst | 4 +-
genomes/human.hg18.genome | 1 +
genomes/human.hg19.genome | 1 +
genomes/human.hg38.genome | 1 +
genomes/mouse.mm10.genome | 67 +++++++
genomes/mouse.mm10.genome.txt | 66 -------
genomes/mouse.mm8.genome | 1 +
genomes/mouse.mm9.genome | 2 +-
scripts/makeBashScripts.py | 1 +
src/annotateBed/annotateBed.cpp | 2 +-
src/bedToBam/bedToBam.cpp | 2 +-
src/bedpeToBam/bedpeToBam.cpp | 2 +-
src/bedtools.cpp | 9 +-
src/closestFile/Makefile | 1 +
src/complementFile/Makefile | 1 +
src/complementFile/complementFile.cpp | 33 +++-
src/complementFile/complementFile.h | 5 +-
src/coverageFile/Makefile | 1 +
src/coverageFile/coverageFile.cpp | 3 -
src/coverageFile/coverageFile.h | 1 +
src/fastaFromBed/fastaFromBed.cpp | 103 ++++++----
src/fastaFromBed/fastaFromBed.h | 6 +-
src/fastaFromBed/fastaFromBedMain.cpp | 35 ++--
src/fisher/fisher.cpp | 2 +-
src/fisher/kfunc.cpp | 2 +-
src/genomeCoverageBed/genomeCoverageBed.cpp | 57 +++++-
src/genomeCoverageBed/genomeCoverageBed.h | 5 +
src/genomeCoverageBed/genomeCoverageMain.cpp | 27 +++
src/groupBy/Makefile | 1 +
src/intersectFile/Makefile | 1 +
src/intersectFile/intersectFile.cpp | 28 ++-
src/jaccard/Makefile | 1 +
src/mapFile/Makefile | 1 +
src/mergeFile/Makefile | 1 +
src/regressTest/RegressTest.cpp | 2 +-
src/sampleFile/Makefile | 1 +
src/sampleFile/sampleFile.cpp | 2 +-
src/{bedToIgv => shiftBed}/Makefile | 8 +-
src/shiftBed/shiftBed.cpp | 77 ++++++++
src/{slopBed/slopBed.h => shiftBed/shiftBed.h} | 26 ++-
.../slopBedMain.cpp => shiftBed/shiftBedMain.cpp} | 101 +++++-----
src/shuffleBed/shuffleBed.cpp | 112 +++++------
src/shuffleBed/shuffleBed.h | 6 +-
src/shuffleBed/shuffleBedMain.cpp | 2 +
src/slopBed/slopBed.cpp | 75 +++++---
src/spacingFile/Makefile | 1 +
src/subtractFile/Makefile | 2 +-
src/subtractFile/subtractFile.cpp | 16 +-
src/utils/BinTree/BinTree.cpp | 5 +-
src/utils/BinTree/BinTree.h | 4 +-
src/utils/BinTree/Makefile | 1 +
src/utils/Contexts/ContextBase.cpp | 11 +-
src/utils/Contexts/ContextBase.h | 3 +-
src/utils/Contexts/ContextCoverage.cpp | 1 +
src/utils/Contexts/ContextGroupBy.cpp | 2 +-
src/utils/Contexts/ContextIntersect.cpp | 23 ++-
src/utils/Contexts/ContextIntersect.h | 10 +
src/utils/Contexts/Makefile | 1 +
.../FileReaders/BufferedStreamMgr.cpp | 2 +-
src/utils/FileRecordTools/FileReaders/Makefile | 3 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 98 +++++-----
.../FileReaders/SingleLineDelimTextFileReader.h | 2 +
src/utils/FileRecordTools/Makefile | 1 +
.../FileRecordTools/Records/Bed12Interval.cpp | 16 +-
src/utils/FileRecordTools/Records/Bed12Interval.h | 3 +-
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 1 -
src/utils/FileRecordTools/Records/Bed4Interval.cpp | 2 +-
src/utils/FileRecordTools/Records/BlockMgr.cpp | 18 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 3 +-
src/utils/FileRecordTools/Records/GffPlusRecord.h | 2 +-
src/utils/FileRecordTools/Records/GffRecord.cpp | 2 +-
src/utils/FileRecordTools/Records/GffRecord.h | 1 +
src/utils/FileRecordTools/Records/Makefile | 3 +-
src/utils/FileRecordTools/Records/Record.cpp | 3 -
src/utils/FileRecordTools/Records/Record.h | 3 +
.../FileRecordTools/Records/RecordKeyList.cpp | 6 +-
src/utils/FileRecordTools/Records/RecordKeyList.h | 6 +-
.../FileRecordTools/Records/RecordKeyVector.cpp | 6 +-
.../FileRecordTools/Records/RecordKeyVector.h | 6 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 1 +
src/utils/GenomeFile/NewGenomeFile.cpp | 4 +-
src/utils/KeyListOps/KeyListOps.cpp | 11 +-
src/utils/KeyListOps/KeyListOpsMethods.cpp | 28 +--
src/utils/KeyListOps/Makefile | 1 +
src/utils/NewChromsweep/CloseSweep.cpp | 13 +-
src/utils/NewChromsweep/Makefile | 1 +
src/utils/NewChromsweep/NewChromsweep.cpp | 42 ++---
src/utils/RecordOutputMgr/Makefile | 1 +
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 123 ++++++------
src/utils/RecordOutputMgr/RecordOutputMgr.h | 3 +-
src/utils/ToolBase/Makefile | 1 +
src/utils/bedFile/bedFile.cpp | 123 ++++++------
src/utils/bedFile/bedFile.h | 11 +-
src/utils/bedFilePE/bedFilePE.cpp | 8 -
src/utils/driver/Makefile | 1 +
src/utils/fileType/FileRecordTypeChecker.cpp | 51 ++---
src/utils/fileType/FileRecordTypeChecker.h | 1 +
src/utils/general/ParseTools.cpp | 3 +-
src/utils/general/ParseTools.h | 2 +-
src/utils/general/Tokenizer.cpp | 150 ++++++++-------
src/utils/general/Tokenizer.h | 9 +-
src/utils/version/version_release.txt | 6 +-
src/windowMaker/windowMaker.cpp | 36 +++-
src/windowMaker/windowMakerMain.cpp | 7 +-
test/closest/dmr.bed | 1 +
test/closest/islands.2.bed | 1 +
test/closest/islands.bed | 1 +
test/closest/kclosest/test-kclosest.sh | 4 +-
test/closest/null_a.bed | 4 +
test/closest/null_b.bed | 1 +
test/closest/null_c.bed | 1 +
test/closest/shores.bed | 1 +
test/closest/test-closest.sh | 50 +++++
test/closest/tfbs.bed | 1 +
test/complement/test-complement.sh | 116 ++++++++++++
test/coverage/c.bed | 2 +
test/coverage/one_block.bam | Bin 0 -> 234 bytes
test/coverage/sam-w-del.bam | Bin 0 -> 225 bytes
test/coverage/test-coverage.sh | 209 ++++++++++++++++++++-
test/coverage/three_blocks.bam | Bin 0 -> 239 bytes
.../{intersect => coverage}/three_blocks_match.bam | Bin
test/coverage/two_blocks.bam | Bin 0 -> 237 bytes
test/coverage/x.bed | 3 +
test/coverage/y.bed | 1 +
test/fisher/get.sh | 2 +
test/fisher/test-fisher.sh | 2 +-
test/general/test-general.sh | 19 +-
test/genomecov/chip.sam | 4 +
test/genomecov/genome.txt | 3 +
test/genomecov/pair-chip.sam | 4 +
test/genomecov/test-genomecov.sh | 23 ++-
test/getfasta/test-getfasta.sh | 58 ++++--
test/groupBy/test-groupby.sh | 9 +
test/intersect/a.issue311.bed | 1 +
test/intersect/b.issue311.gff | 1 +
test/intersect/b.issue311.vcf | 3 +
test/intersect/blocks.bed12 | 4 +
test/intersect/bug223_e.vcf | 3 +-
test/intersect/gdc.gff | 24 +--
test/intersect/new_test-intersect.sh | 82 +++++++-
test/intersect/null_a.bed | 4 +
test/intersect/null_b.bed | 1 +
test/intersect/null_c.bed | 1 +
test/intersect/test-intersect.sh | 185 ++++++++++++++++--
test/makewindows/a.19bp.bed | 1 +
test/makewindows/a.20bp.bed | 1 +
test/makewindows/a.33bp.bed | 1 +
test/makewindows/test-makewindows.sh | 84 +++++++--
test/map/.RData | Bin 0 -> 77 bytes
test/map/.Rhistory | 6 +
test/map/test-map.sh | 20 +-
test/map/test.gff | 12 +-
test/merge/test-merge.sh | 16 +-
test/{flank => shift}/a.bed | 0
test/shift/test-shift.sh | 115 ++++++++++++
test/{flank => shift}/tiny.genome | 0
test/shuffle/incl.sizedif.bed | 4 +
test/shuffle/test-shuffle.sh | 9 +
test/slop/a.bed | 1 -
test/test.sh | 3 +
tutorial/bedtools.html | 2 +-
172 files changed, 2294 insertions(+), 880 deletions(-)
create mode 100644 docs/content/images/tool-glyphs/barski_binding_site.png
create mode 100755 docs/content/tools/shift.rst
mode change 100755 => 100644 genomes/human.hg18.genome
mode change 100755 => 100644 genomes/human.hg19.genome
create mode 100644 genomes/mouse.mm10.genome
delete mode 100644 genomes/mouse.mm10.genome.txt
mode change 100755 => 100644 genomes/mouse.mm8.genome
mode change 100755 => 100644 genomes/mouse.mm9.genome
mode change 100644 => 100755 scripts/makeBashScripts.py
copy src/{bedToIgv => shiftBed}/Makefile (85%)
create mode 100644 src/shiftBed/shiftBed.cpp
copy src/{slopBed/slopBed.h => shiftBed/shiftBed.h} (63%)
copy src/{slopBed/slopBedMain.cpp => shiftBed/shiftBedMain.cpp} (60%)
create mode 100644 test/closest/dmr.bed
create mode 100644 test/closest/islands.2.bed
create mode 100644 test/closest/islands.bed
create mode 100644 test/closest/null_a.bed
create mode 100644 test/closest/null_b.bed
create mode 100644 test/closest/null_c.bed
create mode 100644 test/closest/shores.bed
create mode 100644 test/closest/tfbs.bed
create mode 100644 test/complement/test-complement.sh
create mode 100644 test/coverage/c.bed
create mode 100644 test/coverage/one_block.bam
create mode 100644 test/coverage/sam-w-del.bam
create mode 100644 test/coverage/three_blocks.bam
copy test/{intersect => coverage}/three_blocks_match.bam (100%)
create mode 100644 test/coverage/two_blocks.bam
create mode 100644 test/coverage/x.bed
create mode 100644 test/coverage/y.bed
create mode 100644 test/fisher/get.sh
create mode 100644 test/genomecov/chip.sam
create mode 100644 test/genomecov/genome.txt
create mode 100644 test/genomecov/pair-chip.sam
mode change 100644 => 100755 test/genomecov/test-genomecov.sh
create mode 100644 test/intersect/a.issue311.bed
create mode 100644 test/intersect/b.issue311.gff
create mode 100644 test/intersect/b.issue311.vcf
create mode 100644 test/intersect/blocks.bed12
create mode 100644 test/intersect/null_a.bed
create mode 100644 test/intersect/null_b.bed
create mode 100644 test/intersect/null_c.bed
create mode 100644 test/makewindows/a.19bp.bed
create mode 100644 test/makewindows/a.20bp.bed
create mode 100644 test/makewindows/a.33bp.bed
create mode 100644 test/map/.RData
create mode 100644 test/map/.Rhistory
copy test/{flank => shift}/a.bed (100%)
create mode 100644 test/shift/test-shift.sh
copy test/{flank => shift}/tiny.genome (100%)
create mode 100644 test/shuffle/incl.sizedif.bed
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