[med-svn] [bedtools] branch debian/unstable updated (b0cdd10 -> 854dcc2)
Charles Plessy
plessy at moszumanska.debian.org
Thu Jul 7 04:53:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository bedtools.
from b0cdd10 Current changelog entry.
adds 554c097 Fixed bug281: -S not working in closest. Added unit tests.
adds e84011c Addressed bug 268: slowdown with -iu
adds b03556e still working on bug268, progress made
adds 7ba9c36 More fixes to closest for bug268; disallowed stranded ops on unstranded files for all tools.
adds be44824 don't raise a chromosome discrepancy error for unmapped reads in BAM dbs.
adds 2f3ef74 tabs to spaces.
adds 96a2d84 update conf.py to avoid sphinx build error on RTD.
adds 788a6b6 handle null record when db is bed6+. affected -wao, -loj, closest.
adds 93cb0b1 remove memory leak in NewChromSweep::closeOut
adds f66a564 Update README.md
adds 11640d8 Update README.md
adds c3ba7be Update README.md
adds 285c3ac Update README.md
adds 0686eea Merge branch 'master' of https://github.com/arq5x/bedtools2
adds d22594e Check for non-empty vector
adds 7f765bc Merge pull request #306 from gatoravi/master
adds 6de430d issue #303. fix memory leak in groupby.
adds 61b9c41 Merge remote-tracking branch 'upstream/master'
adds ef9f42a Fixed bug #317, groupBy failed to recognize integers with decimals
adds f9ef58f General fix for #317 - for groupBy, override non-bam files' type
adds e392a61 Merge pull request #294 from nkindlon/master
adds 7c36bfa fix memory leak during sweep's closeOut of DB files.
adds b35341c Move "using namespace std" after #includes
adds 67aca77 Use ostringstream to format filename
adds 3d31735 Merge pull request #320 from jmarshall/warnings4
adds 97a2235 Added chrMT, fixed genome name
adds 6cca09e LF line endings, 644 file mode genomes
adds d2d9c95 Added mm10 chrMT entry
adds 0836fed Merge pull request #289 from LukeGoodsell/feature/chrMT
adds c99baef Merge branch 'master' of https://github.com/arq5x/bedtools2
adds a86243d BAM files, genomecov pair-end fragment size, or fixedFragment size -pc -fs
adds 728e07a BUG Fix
adds b401c43 Check if right side goes below 0
adds a8162a6 Documentation added - corrected binding for start end
adds 02e48c2 Merge pull request #318 from SciDAP/master
adds 9b34f4b Fixes #334. Remove extraneous tab from BED4::printNull(). Thanks to @dwaggott.
adds f91a32d Fixes #329. groupby handles single column input.
adds 95655a0 Fixes #321. Enable freqasc and freqdesc in groupby.
adds 98b4402 tab delimited mm10
adds e4c5e55 update installation instructions to use github.
adds d188b65 fix double comparisons to zero
adds 6d3fcbc fix typo in closest doc glyph
adds 78d74e9 -r should force the value for -F for intersect.
adds 22f445a Allow for overwriting the prefix
adds 8107e8a Merge pull request #345 from bgruening/patch-1
adds bb7cbfe Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 9b734e6 missing null printing for GffPlusRecords.
adds a307830 show help if solely sub-command is given.
adds d6e2ae4 restore -grp, -opCols and -ops to groupby. Resolves #300
adds 2bbe124 add -bedOut option to getfasta
adds 4e1b658 remove -fo from getfasta. always go to stdout.
adds fe3bd3f fix null reporting with multiple db files.
adds 1ae009d add tests
adds 44ca4e9 one too few tabs in annotate -names
adds f2f521d #325 allow -s and -w to b used in any order for makewindows
adds 6b75c05 add a 'shift' tool
adds 1f27837 document shift tool
adds 9bab0f9 update authorship
adds 91ffc1d test for shifts greater than signed int
adds 6d8db56 Add shift tests to test scripts
adds de9b06a move shift size calc to AddShift
adds f250e10 Merge pull request #350 from davidrichardson/dr_shift
adds f09d845 Changed expected output for merge.t11 to reflect the current output of merge. The test now passes.
adds 5b590f9 Merge pull request #328 from skotchandsoda/master
adds baa5137 Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 89cde77 try to fix gcc5+ errors and silence various warnings.
adds a3e17ca fix getfasta tests in light of the removal of -fo
adds 447c995 fix getfasta tests to account for removal of -fo option
adds 401c61d update docs for -dz
adds 577fecf fix for issue #356
adds af82217 enable stdev and sstdev for groupby. fixes issue #367
adds 5e293d4 use STL tokenizer to split on ','. Addresses #366
adds a64248d Merge branch 'issue_366'
adds d3f4654 add test for issue 366
adds b2615f8 Fix KeyListOps stddev and min/max methods
adds 5e7c696 Merge pull request #369 from jmarshall/KeyListOps
adds 42abf50 cleanup
adds 8dfe9b8 complement: check intervals agains chrom len. resolves #376
adds f96fcd8 Allow debug builds in Makefile.
adds 1305e92 Merge pull request #375 from yesimon/make_debug
adds 3508355 add long stuff found by @ryanlayer's compiler settings.
adds 9966011 Merge pull request #379 from brentp/fisher-long
adds a5ea332 Merge branch 'master' of https://github.com/arq5x/bedtools2
adds e9e6b9a shuffle: warn when ivl exceeds max chrom length. Fixes #377
adds 25cf6fd Fix complement segfault for empty input intervals.
adds fddd08a merge pull #374
adds 76b36e2 Merge branch 'yesimon-complementfile_empty'
adds 1b2443b Fix typo in docs
adds 671d044 Merge pull request #380 from rmzelle/patch-1
adds c1dbdd6 Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 7b930d9 coverage: correctly compute depth for -split. resolves #354
adds b0328c3 update tutorial link.
adds 28a2f5c Remove excess const from function return types
adds 7c6fdb7 Fix typo [minor]
adds 2a99966 Merge pull request #382 from jmarshall/intel-warnings
adds 5ee3285 Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 78826cb fix the counting of hit distances in closest.
adds 2523c35 update tests for closest -mdb based on issue reported by Jo on 11-Apr-2016
adds 42b1de1 force makewindows to always create -n windows from a BED record.
adds 8435bd3 weighted includes
adds fe1eabe Merge pull request #386 from zeeev/master
adds 34913f2 Minor typo correction in documentation
adds ee72249 Merge pull request #399 from keithcallenberg/patch-1
adds 76faa3b Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 3d027c9 Addresses #311. fix off by one error when reporting overlaps with VCF or GFF.
adds dfff6ba Address #316. Handle both SVLEN and END
adds cc3fb42 don't delete testing bams
adds fbf2686 resolve further off by one errors when intersecting GFF/VCF and BED
adds cf975b2 Merge branch 'issue_311'
adds 066075b prevent underflow
adds ef73e6e handle multiple, posibble negative SVLENs. choose abs_max.
adds 9bfce2d fix map's stdev and sstdev tests
adds 3d1831e update general tests
adds 780faf7 fix broken SV intersect test
adds e51b337 restore -fo option to getfasta for backwards compatibility.
adds e88e919 tweak test file.
adds 5e87af7 Tip for extracting single region BED files
adds e79e3cb Merge pull request #403 from s-boardman/patch-1
adds a0dc5db Fixes #407. Force coverage to process every record in query file.
adds 5c0e33a first pass
adds 17c2172 restore help with -h or --help
adds b432a31 cleanup
adds 548a3c6 fix for issue #336
adds e67accc Added feature: name, chromosome and position in fasta headers #406
adds 9e51614 Merge pull request #410 from rishavray/feature/#406getfasta
adds 2285e98 add tests for getfasta
adds f060164 Fix BedFile::GetNextBed()'s handling of missing newlines
adds 5de3a9b Merge pull request #404 from jmarshall/fix-GetNextBed
adds c8604e9 update docs for 2.26.0
adds b7b2b72 update docs version
adds f7d3b7e add -pc to history
adds 872220a Setting Release-Version v2.26.0
adds 3b91220 cleanup
adds a525d82 Setting Release-Version v2.26.0
adds e6f27ac missing test files
adds 99bead1 missing test files
adds 1e16d52 Setting Release-Version v2.26.0
new 854dcc2 Merge tag 'v2.26.0' 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 | 29 +-
README.md | 15 +-
docs/conf.py | 8 +-
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/groupBy/groupBy.cpp | 8 +-
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/split/splitBed.cpp | 11 +-
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 | 43 +-
src/utils/Contexts/ContextBase.h | 5 +-
src/utils/Contexts/ContextCoverage.cpp | 1 +
src/utils/Contexts/ContextGroupBy.cpp | 2 +-
src/utils/Contexts/ContextIntersect.cpp | 27 +-
src/utils/Contexts/ContextIntersect.h | 10 +
src/utils/Contexts/ContextJaccard.cpp | 20 -
src/utils/Contexts/ContextMerge.cpp | 11 +-
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/FileRecordMgr.cpp | 11 +-
src/utils/FileRecordTools/FileRecordMgr.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/PlusFields.h | 4 +-
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 | 326 ++++++-----
src/utils/NewChromsweep/CloseSweep.h | 39 +-
src/utils/NewChromsweep/Makefile | 1 +
src/utils/NewChromsweep/NewChromsweep.cpp | 623 +++++++++++----------
src/utils/RecordOutputMgr/Makefile | 1 +
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 130 ++---
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 | 58 +-
src/utils/fileType/FileRecordTypeChecker.h | 1 +
src/utils/general/ParseTools.cpp | 18 +-
src/utils/general/ParseTools.h | 3 +-
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/bug281_a.flip.medium.bed | 2 +
test/closest/bug281_a.medium.bed | 2 +
test/closest/bug281_b.bed | 4 +
test/closest/bug281_b.flip.bed | 4 +
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 | 148 +++++
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 +-
185 files changed, 3017 insertions(+), 1352 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/bug281_a.flip.medium.bed
create mode 100644 test/closest/bug281_a.medium.bed
create mode 100644 test/closest/bug281_b.bed
create mode 100644 test/closest/bug281_b.flip.bed
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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