[med-svn] [bedtools] annotated tag 2.26.0+dfsg created (now 5f97d86)
Andreas Tille
tille at debian.org
Mon Jul 18 14:51:16 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to annotated tag 2.26.0+dfsg
in repository bedtools.
at 5f97d86 (tag)
tagging f2b5aa1b9c4ef7fc07a1dfde126177ec7f9cb6a1 (commit)
tagged by Andreas Tille
on Mon Jul 18 16:06:21 2016 +0200
- Log -----------------------------------------------------------------
Upstream version 2.26.0+dfsg
Aaron (766):
Added "inspan" and "outspan" to peIntersectBed
Updated USAGE_EXAMPLES to include peIntersectBed
Updated master Makefile and fixed bug in genomeCoverage
Removed extraneous testing files.
BEDTools Public Release 2.0
Updated documents to say Version 2.0
Added UCSC browser header support. Fixed bug in mergeBed. Release 2.0.1
Updated VERSION and removed extraneous files.
Allowed empty lines in bedFile.cpp
Updated version.h to 2.0.1
Fixed bug in peIntersectBed when using stdin.
VERSION 2.1.0
Changed BED.score to int from ushort
Changed BEDPE.score to int from ushort
Version 2.1.1
Updated ancillary files for Version 2.1.1
Updated the help message for fastaFromBed
Changed the score field to be a string to allow greater BED flexibility.
Fixed bug with parsing name field in bedFile.cpp
VERSION 2.1.2
Version 2.2.0
Added -names feature to mergeBed
Simple changes.
Reomved test files from intersectBed
Release 2.2.1
Improved the speed of genomeCoverageBed by roughly 100 fold.
Indicated that genomeCoverageBed requires sorted/grouped input.
Version 2.2.3
Changed windowBed help message.
Version 2.2.4 (10/27/2009)
Updated BED entry sanity checking.
Replaced cout with printf for speed in bedFile.h
Added slopBed, shuffleBed and maskFastaFromBed.
Added initial, untested version of pairToPair
Added working version of pairToPair and sanity checked all tools versus previous version.
Added gffToBed and samToBed
Version 2.3. Just before paper submission.
Version 2.3.1
Version 2.3.1 (for real)
Version 2.3.2 (11/25/2009)
Added new logic to handle stdin or file in slopBed.
Version 2.3.3 (12/17/2009)
Added initial cut at BED12 support.
GFF support seems to work. Improved bedFile.cpp.
Fixed intersectBed to be 80 chars wide.
Updated windowBed to 80 char width.
Multiple changes to intersect and window
Updated closestBed
Updated subtractBed
Updated mergeBed and bedFile.cpp
Updated coverageBed and bedFile.cpp
Updated genomeCoverageBed.
Updated fastaFromBed.
Updated maskFastaFromBed.
Updated shuffleBed, slopBed, sortBed and linksBed.
Fixed pandemic bug in main loop logic that we corrupting BED entries.
Improved binKeeperFind logic.
Generalized binKeeperFind to FindOverlapsPerBin
Added initial BAM support to intersectBed
Added bamToBed.
Initial BAM support for pairToBed
Imporved BAM support in pairToBed
Updated pairToPair.
Cleaned up bedFile.h and added -m64 to Makefiles
Command line option formatting standardized.
Further standardization of the option listings.
Fixed bug in complementBed vis-a-vis Galaxy.
Added +1 to start reporting for GFF features.
Fixed bug in mergeBed causing names to be reported twice
Added mate to name and mapqual as score in intersectBed.
Removed -m64 from Makefiles.
Added -outbam check to intersectBed
Added sanity check to pairToBed
Updated BEDPE reporting strategy for BAM files.
Added support to BEDPE to allow optional fields at the end.
Added check to fastaFromBed preventing sequences from being
Fixes to fastaFromBed maskFastaFromBed
Fixed -type notboth in pairToBed when using -bedpe.
Fixed tar goof.
Cleanup after testing.
Fixed intersectBed Makefile and changed README.
Added example files to /data.
Added BEDTools manual to distribution.
Updated HISTORY.
Cleaned up files from master.
Added /data.
Added files to /data
Removed extraneous data file from src/bamToBed.
Removed extraneous genome file.
Added Derek's changes to BamTools that were causing compile errors.
Updated manual.
Fixed bug in mergeBed that caused segfault when -nms and -s used together.
Corrected commnad line parsing for all tools.
Updated version to 2.4.2
Added manual.
Fixed bug in pairToBed and removed tr1 include.
Fixed command line bug in bamToBed.
Added BED+ support and improved GFF/BED distinction.
Version 2.5.0
Fixed line parsing bug.
Version 2.5.2 (Feb-2-2010)
Changed "notboth" logic in pairToBed when inout is BAM.
Fixed several bugs and improved BAM performance.
Version 2.5.3 (Feb-19-2010)
Fixed compilation warning in bamToBed.cpp
Version 2.5.4 (Mar-3-2010)
Fixed bug in mergeBed that screwed up the names tracked for merged entries.
Fixed yet another bug in the -nms option in mergeBed.
Update to fastaFromBed and intersectBed.
Corrected logic for type=notboth using BED in pairToBed.
Improvements to coverageBed
Now tracking bin/ and src/
Trying to force bin/ and obj/ to make it to G.C.
Added new program: overlap
Initial support for BED12 output in bamToBed.
Renamed end to alignmentEnd in bamToBed
Corrected -bed12 logic in bamToBed. Thanks to Ann Loraine for test data.
Added check to Bedfile::parseLine to return false when a blank line is encountered.
Added BEDGRAPH functionality to genomeCoverageBed. From Gordon Assaf, CSHL.
Added native BAM support to coverageBed.
Added native BAM support to genomeCoverageBed.
Updated Makefiles for coverageBed and genomeCoverageBed
Added genomeFile class and updated genomeCoverageBed to use it.
complementBed now uses the GenomeFile class.
shuffleBed now uses the GenomeFile class.
slopBed now uses the GenomeFile class.
Final changes for 2.6.0
Addeed newlines to end of genomeCoverageBed.cpp and overlap.cpp
Fixed a careless command line parsing bug in coverageBed.
Added the -wao option to intersectBed.
First cut at bedToBam. Gordon is testing it.
Updated bamToBed to include new AlignmentEnd method.
Resolved the branch merge conflicts with the zlib branch.
Updated bedFile Makefile for gzstream
Added gzstream to bedFile.
Updated all Makefiles for gzstream support.
Added new version of BamTools and fixed a couple minor bugs in intersectBed that were caused by the branchmerge.
Updated most of the code to use _ notation and the Open,GetNext,Close functionality.
Updated all of the tools to use the Open/Get/Close idiom.
Reset bedEntry to nullBed in all Open/Get/Close loops. Clears out data from previous entry.
Several changes:
Added NULL terminator to AddBamTag() in BamAux.h
Fixed bugs in bamToBed.
Multiple changes.
Updated usage statement for pairToBed.
Added zlib support and Open/Get/Close idiom to pairTo*.
Revised the Open/Get/Close idiom to check for BED_VALID on each iteration.
Updated Makefiles to use -O2 instead of -O3.
Fixed segfault in genomeCoverageBed cuased when BEDs have a chrom not in GENOME.
Added -bga mode to genomeCoverageBed. Thanks to Gordon Assaf, CSHL.
Improved help message for genomeCoverageBed
Added the faulty line number when reporting malformed BED/GFF entries to BedFile::parseLine()
Multiple changes.
Forced proper BEDPE order for bamToBed and pairToBed.
Removed the seq and qual defaults from bedToBam. Thanks to James Ward.
Fixed bug in processing BED files in coverageBed using the Open/Get/Close idiom.
Added newlines to the end of windowMain.cpp and genomeFile.cpp
Fixed chrom allocation bug in genomeCoverageBed.
Fixed bug in sortBed that caused the output to be written twice.
Added Open() to BedWindow::WindowIntersectBed().
Added Open() idiom to BedSubtract::SubtractBed().
Updated version and RELEASE_HISTORY to reflect v2.7.0.
Fixed constructor definition in closestBed.h. Caused compilation issues for Gordon Assaf.
Fixed a typo that caused some compilers to fail on closestBed.
Large, performance-related commit.
Added gzstream to master branch
Improved fastaFromBed.
Large commit
Added splitBedIntoBlocks and first pass at "blocked" intersection in intersectBed.
Added split BAM functionality to intersectBed and coverageBed.
Added bed12ToBed6
Multiple changes.
Added bedToIgv.
Minor stylistic tweaks.
Fixed logic relating to "split" coverage.
Fixed string references for strand (i.e. '+' to "+") in windowBed and pairToBed.
Large commit.
Fixed bug in groupBy and added logic to enforce that strings are numeric when asking for nueric ops.
Added slop to filename when using -slop in bedToIgv.
Added newline to end of BamAncillary.cpp to avoid compile warnings.
Added newline to end of BamAncillary.h
Updated RELEASE_HISTORY.
Tweaked the includes in tabFile.h and groupBy.cpp
Added bedToIgv to the release.
Improved the usage statement for groupBy and bedToIgv.
Created an "either" mode for pairToPair.
Updated the pairToPair usage statement.
Tracking the tabFile Makefile.
Fixed a bug in bedFile.h preventing GFF strands from being read properly.
Fixed bug in intersectBed causing -r to not report the same result when files are swapped.
Added checks to groupBy to prevent the selection of improper opCols and groups.
Removed omp.h include from bedToBam.
Fixed compilation issues with groupBy and bedToIgv.
Updated the usage statements to reflect bed/gff/vcf support.
Defined the name field for VCF files.
Fixed bug in FindOneOrMoreOverlapsPerBin.
Updated overlap usage statement.
Added fileType.cpp to auto-detect gzipped files (Thanks to Assaf Gordon.)
Changes to RELEASE_HISTORY and VERSION and chmods
Fixed bug in Makefiles calling fileType.o "filetype.o"
Undid a stupid change I made to BGZF.cpp
Resetting the master from stupid little changes.
Added <cctype> includes to BamAux.h and sequenceUtilities.h
Added GetTag logic for bamToBed
Fixed bug in detecting whether or not columns are numeric.
Fixed bug in parsing lines that caused some GFF files to be detected as VCF.
Multiple changes.
Fixed bug preventing closest feature detection for features with start < 2048000.
Fixed bug reporting in either mode for pairToPair.
Changed UINT from 16 bit to 32 bit in bedFile. Resolves issue 21.
Fixed overflow bug in slopBed causing starts and ends beyod the size of the chrom.
Added per base coverage (-d) to coverageBed and cleaned up the main loop.
Added feature to get distance to closest feature (-d). Thanks to Erik Arner.
Minor tweaks.
First commit for unionBedGraphs and multi-column groupBy.
Improved the error checking for unionBedGraphs.
Cleaned up groupBy and unionBedFiles.
Updated version.
Updated the unionBedGraphs help.
Updated groupBy examples.
Big commit.
Large update to groupBy.
Updated BED struct for future fjoin alg. support.
GroupBy defaults to stdin and uses -g -c -o as well.
bamToBed assumes stdin.
bed12ToBed6 assumes stdin.
bedToBam assumes stdin.
bedToIgv assumes stdin.
complementBed assumes stdin.
linksBed assumes stdin.
mergeBed assumes stdin.
overlap assumes stdin.
shuffleBed assumes stdin.
slopBed assumes stdin.
sortBed assumes stdin.
Changed precision for groupBy.
annotateBed can report counts and pct coverage for each annotation file.
Added -ubam support to intersectBed and bedToBam.
windowBed supports -ubam.
Added -ubam to pairToBed.
Fixed initialization bug in annotateBed constructor.
Update GPL license in source banners.
Updated version to 2.10.0
Updated release history to reflect 2.10.0
Updated Makefile
Removed careless debugging message from annotateBed.
Added the -cigar option to bamToBed.
Tweaked hep for bamToBed
Fixed pairToPair to allow full "B" entries to be reported in every mode.
Merge branch 'pairToPair_update'
Updated version to 2.10.2
Prettied up the code before pushing to github.
Updated Makefile to auto-create obj/ and bin/.
Tweaked Makefile.
Tabs in Makefile.
Added bedGraphFile's Makefile.
Changed BamAlignmentSupportData from private to public.
Fixed casting issue in windowBed.AddWindow() that cuased slop positions to run off the end of the chromosome.
Allowed 8 or 9 column GFF/GTF files. Many thanks to Michael Hoffman.
Minor formatting in slopBed.cpp.
Revising README to README.rst
Playing with README.
Playing with README.
Playing with README.
Playing with README.
Playing with README.
Playing with README.
Fixed Issue #59.
Fixed Issue #60. Improved randomization granularity for shuffleBed.
Seeding shuffleBed with srand((unsigned)time(0)+(unsigned)getpid()); Thanks to Rob Long.
Added support for zero length features (start = end, e.g. insertions in ref genome).
Removed groupBy from the BEDTools distribution.
Tweaked fjoin reporting.
Fixed reporting bug for zero-length overlaps.
Added size() method to BED struct.
Issue #50. SlopBed now adds percent-based slop to features with the -pct option.
Improvements to shuffleBed, including:
Tweaked commenting in shuffleBed.
gzstream Makefile now inherits compilation flags from master Makefile.
Fixed issue #55: mergeBed now reports 1-based starts for GFF files. Also,
Version 2.11
Updated RELEASE_HISTORY to reflect version 2.11.0
Fixed issue #62. Incorrect start and end coordinates for BEDCOV structs.
Added newline to BamIndex.h
Fixed a casting issue in slopBed.
Version = 2.11.1
complementBed now uses vector<bool> instead of vector<short>
Added complementBed.h
MergeBed now correctly handles a max distance "-d" parameter.
Version 2.11.2
Fixed -wao and -wo in intersectBed for zero-length features.
Added -score option to mergeBed and allowed duplicate names for -nms option.
mergeBed complains when no names or scores are present for -nms and -scores.
Fixed bug in shuffleBed incorrectly disallowing a lack of -incl and -excl.
The output of fastaFromBed is now in the order of the input -bed file.
fixed bug in shuffleBed when using -incl.
Added option to report block number as score in bed12ToBed6
Made bedToIgv filenames Windows friendly. Thanks to Jiam Wang
Optionally set masking character (-mc) in maskFastaFromBed. Thanks to Can Alkan.
Fixed bug in closestBed when B feature's end equal to A feature's start.
Tweaked an error message in genomeCoverageBed.
Added new flankBed tool.
Updated flankBed help
Corrected stranded logic for + features in flankBed.
Removed Eclipse files.
Unmapped BAM alignments are now captured by -v in intersectBed and windowBed. Thanks to Davide Cittaro.
Fixed overlflow error in pairToPair
logical, not operator. need coffee.
Defaults for BED constructors. Cheers to John Marshall for the catch.
Defaults to other constructors.
Improved clarity for zero length features in coverageBed.
Updated version and RELEASE_HISTORY for 2.12.0
fastaFromBed warns of exceeding length of chromosome and of zero length features.
Tweaked Makefile and added notboth option to pairToPair.
First cut at nucBed - profiles DNA sequences defined by BED intervals.
Added -5, -3, -trackline, -trackopts, and -dz options to genomeCoverageBed. Many thanks to Assaf Gordon.
mergeBed now _always_ reports in BED format (i.e., zero-based starts), regardless of input type.
Improvements to closestBed. Thanks to suggestions by Brent Pedersen, Ryan Layer, Assaf Gordon, Dan Webster.
Added output description to nucBed help
header and custom pattern search for nucBed. Thanks to Can Alkan.
Tweaked header in nucBed
Patched Assaf Gordon's tweaks to gCB.
Fixed multi-line UCSC mysql query in the help for multiple tool. Thanks to Brent Pedersen\!
Further tweak to UCSC mysql help.
Changed newline to tab in bamToBed for -tag -bed12.
Added BamTools-Ancillary files
New BamTools 1.0 project structure and Makefile
preliminary support for bamtools1.0 for bamToBed.
bedToBam links with bamtools1.0
coverageBed links with bamtools1.0
intersect, window, and gcB support for bamtools1.0
removed multiBamCov from main Makefile
Set BAM compression mode before opening
bamtools GetEndPosition() now defaults to unpadded, zero-based
specifically request unpadded and 1-based ends from GetEndCoordinate()
Hooray, support for BamTools 1.0. Many good things to come.
First cut at new multiBamCov tool. I like.
aded Bamtools/lib
aded Bamtools/lib
make Bamtools/lib on the fly
make Bamtools/lib on the fly
Tweaked Makefile and using GetNextAlignment() in multiBamCov.
Clean Bamtools objects
Added BamTools object cleanup to the Makefile.
Added minQual (-q) and force proper pairs (-p) to multiBamCov.
multiBamCov tweak
Added -counts option to coverageBed to only collect the count of overlaps (no pct., etc.)
Pushed tagBam to GitHub
Added -f to tagBam.
Updated tagBam help so that it actually works...
Code gussying
Moved FastaHack to the utils/ directory
User can define their own tag type for tagBam.
Updated to 2.13.0.alpha
New region checks for multiBamCov. Thanks to Derek Barnett.
Cleanup of bamtools directories and updated Make
Don't track BamTools/include
Latest BamTools. Commit 525fc971414d7f7b8b60
Updated Makefile for 64bit BAM seeks.
Updated help messages
Changed version number
tweak to Fasta.cpp
15% speedup for the tokenizer.
Tweaks to Tokenize(), GetNextBed(), and detection of negative coordinates. Thanks to @agordon
included cstdlib in lineFileUtilities.h. Thanks to @daler
Merge branch 'master' of github.com:arq5x/bedtools
corrected a pull goof
First cut at -scale for genomeCoverageBed
Makefile tweak
Corrected start check in parseVcfLine. Thanks to Jan Vogel
Added -full to fastaFromBed
GFF can't have 0-length features.
Added logic to keep dups and failed QC for multiBamCov. Thanks to Chip Stewart.
Added -S (opposite strand) logic to intersectBed
Added -S to coverageBed
Added -S to annotateBed
Added -S to closestBed
Added -S to pairToBed
Added -S to subtractBed
Added -Sm to windowBed
now allow "-" as well as "stdin".
BEDTools now supports FIFOs and named pipes. Many thanks Nate Weeks and Michael Hoffman for the suggestions.
Reverted the -full option in fastaFromBed. Use 06a7e24e294e06258c75 to retain it.
fifo support add'l
Updated fastaFromBed
Need to rewind to start of file after Gzip check.
Gzip detected by file extension. Weak, but only approach that works at this point.
Updated gzip detection. Weaker, but necessary for FIFO support
Proper Gzip check
Reasoning for GZIP detection change.
Avoid deleting bedStream iff stdin
Added -s, -S, and -names to tagBam.
Version 2.13.1: Added -s, -S, and -names to tagBam.
Fixed pairToPair's -type notBoth mode
Added -scores option to tagBam
Added Seek and Rewind (destroy?) to BedFile.
Changed error message when BAM is not qeury sorted in pairToBed
gcB no longer requires a genome file for BAM. New chromsweep tool.
chromsweep demo
chromsweep is now a python-style generator. Big smile\!
chromsweep is a proper tool. Now to make it an iterable class.
Gussy.
Added new -sorted option to intersectBed. No memory and filthy fast.
Added newline before version.h EOF
Updated README
Updated README
Updated README
Updated README
Moved nullBed reset to GetNextBed
clean up chromsweep interface
Reworked the nullBed logic.
removed unused attributes in chromsweep
Fixed major bug in intersectBed -split. Thanks to Sol Katzman.
Fixed mouse.mm9.genome. Thanks to Charles Plessy.
Improved detection of faulty GFF features.
Release 2.13.2
-bed now behaves when using bam input in intersectBed.
fixed -bed in intersectBed with gzipped -b. Thanks to @daler.
Version 2.12.3
Minor updates.
getBamBlocks no longer splits on D CIGAR ops when not wanted.
Tweaked Makefile for proper zlib inclusion
chromsweep no longer overloads results p_q on chrom change.
chromsweep now obeys -s and -S
reserve space up front for chromsweep
Merge branch 'master' of github.com:arq5x/bedtools
Tweaked closestBed help for -D
Undo previous. Dumb.
Version 2.13.4
nucBed now obeys strand'
comments
Missed update of closest B feature to right of A feature.
Removed debugging message.
Added new multiIntersectBed tool. New relase to follow.
Force sorting when using multiIntersectBed
Fixed closestBed help help to be -io instead of -no
Added number of and list of files with coverage to mIB
Prep for 2.14.1
Correct GetNextBed file. Oops.
v2.14.2
Fixed include goof and correct empty coverage
Updated version.
Handle header lines for new version of GetNextBed
Updated banner and help for multiIntersectBed.
No need to force chroms to be sorted. Avoid diff.s b/w chr1 and 1
-novo option in bamToBed
bwa mode
bwa mode
Added r. layer's cluster algorithm -cluster
Merge branch 'cluster'
explain the sorting criteria. it's odd thanks to STL PQ behavior.
minor
Added methods to store and report file headers upon request.
Changes for CSHL course.
Added bedpeToBam Makefile
Makefile tweak.
Added intervals option to tagBam.
Fixed getBamBlocks()
Fiex off-by-one in linksBed.
Added -header to intersect, window, closest, slop, flank.
Added unstaged files.
Merge branch 'read_write_headers'
lineNum is now tracked privately.
Allow headers to start with "chrom"
force ^chrom ^track and ^browser headers to only occur on the first line.
Comments for header logic.
Add'l comments.
Makefile aborts on first error.
rename tool to acvoid conflicts. s/overlap/getOverlap
Use new GetNextBed() interface.
Use new GetNextBed() interface. Redux.
Added -header to sortBed
Removed need for nullBed. clear() otherFields in GetNextBed().
bamToBed -bedpe now handles singletons.
Removed nullBed nonsense.
return true on BLANK
Further nullBed tweaking.
Comment fix.
makefile tweak
preliminary
First pass at new, consolidated CLI.
Removed most version.h includes from sub-tools.
New svn/git/samtools - like bedtools interface.
tweaked menu.
tweaked menu.
acknowledge heng li.
gussy
gussy
gussy
remove superfluous *.o
remove superfluous *.o
to for compat. thx to @jmarshall
Uses C++ string comp. Thx to @jmarshall.
fix
Improvements to CLI.
newline at end of file
banner, include.
shuffleBed now weights by chrom size by def.
wipe away bamtools
updated to bamtools 2.0
Makefile mod.
Change shuffleBed defaults.
uBG and mIB use new Point class.
Handle mutiple UCSC header lines and mid-file headers/comments.
Added makewindows sub-command
Warn only when requested chrom not in FASTA file.
added version to subcommands
Missing include.
Relax pairing req's for bamtobed and pairtobed
added cluster tool. both cluster and merge require sorted files for efficiency.
Added groupby back into the bedtools package.
interface tweak
interface tweaks.
changed return codes.
enh: support for remote [ftp|http] files
overhaul of overlap interface. use allHits() and anyHits().
store all input fields and the indices of "extra" fields.
first basic cut at mapBed
Added new VectorOps class.
Added new ops to mapBed
added mode and antimode to VectorOps
Use -f and -r directly in chromsweep
Use updated chromsweep in intersect and map.
add map/mapBed to scripts
ENH: groupBy now uses VectorOps
Add stdint.h
Add stdint.h
Clearer desc. of mapBed's func. programming origins
First cut at BlockedIntervals class to cleanup spliced BAMs and BED12
Fixed help for groupby. Thanks @daler.
Fixed typo. Thanks @daler.
Inform users that merge reqs. sorted input.
Inform users that map reqs. sorted input. Update default.
Added isBed12 attr. and overlap fraction support for blocked intervals.
bail early if not BEDs in BIN; revert to map from unordered_map
added count_distinct to groupby
bail out early if no ivls in bin
add ranlib to bamtools' makefile. thx to jphn marshall
fix typo
fixed util Makefiles to recompile when header changes
refactored intersect; better -bed support for split BAM alignments
tool makefiles not recompile with changes to header
make windows from ivls in bed files.
tweak to help in makewindows. thanks to @agordon
Added beginnings of regression testing framework.
Makefile tweak
Update BamTools to avoid C++11 complications
Need HttpHeader_p.h as well.
Fix make clean to erase bamtools objects. Thanks to John Marshall.
Merge branch 'google_test'
fix blocked_intervals merge conflicts
greater control over splitting on D or N CIGAR ops.
more tests for intersect
remove unnecessary test files
Mention make test in README
added general file formatting tests
typo
fixed numbered list
fixed VectorOps mode and antimode
fixed VectorOps mode and antimode
added preliminary tests for map
typo
add limits.h to VectorOps for INT_MAX
Makefile tweak; Need newline in BlockedIntervals.h
fix bed12tobed6 block num for - strand.
choose null for mapBed
added multiple new tests
speedup merge -s a bit
Allow input files to have consecutive tabs (i.e., empty fields)
new tool: bedtools random
correct bt random's help
remove additional strand from intersect -bed -abam
fixed bug in merge when using -n and -nms. Cleaned up logic and use VectorOps
added new tests for merge
tweaks to help menus
New tests for slop and flank. Fixed chrom end bug in flank.
Fixed bug preventing proper clustering. max(end) was not being updated.
added tests for cluster
Improved error message for bamtobed.
tweak to Makefile
re-add clean to gitversion make. Thanks to @agordon for the insight.
Added expand tool.
added tests for bedtools expand
typo
minor comments
make stand-alone tool for expand.
groupby now supports - for stdin
expand now supports - for stdin
add -leftjoin option to bedtools intersect
change -leftJoin to -loj. Improve help for intersect
correct -abam/-wb/-bed warning
expand now handles gzipped files w/o .gz extension.
Added -C (case-insensitive) matching to nucBed.
make gitversion optional
s/gitversion/version/
track version_git.h
git point version
git point version
v 2.16.0
add new bamtofastq tool.
go back to gitversion
old version file
wrong includes
added @agordon's new versioning system
Setting Release-Version v2.16.0
HELP: groupby -full uses first ine in group
tweaks to bamtofastq
Setting Release-Version v2.16.0
Setting Release-Version v2.16.1
Makefile tweak
twiddle Makefile
fiddle w/ Makefile
add omitted test dirs for "make test"
support for bedtools existing somewhere other than PATH
Setting Release-Version v2.16.2
fixed logic bug in bedtobam's -bed12 mode.
remove extraneous .o
handle unaligned BAMs with -v
safely handle empty input
prefer empty() over size()
fix off-by-one error in calc. -d for closest
genome file drives BAM header order in bedtobam
-wo -wao -c with -abam force BED output. Thanks to @agordon.
regression tests for -abam w/ [-c | -wao | -wo]
only write to bam if bam output req. with -v
correct missing tab in annotate's header
catch missing chroms for mapped BAM alignments. warn, don't out_of_range()
allow uint32 or int32 -tags
Inital screen for -split overlaps should include the full span of A_i
print bedpe record immediately after unpaired read.
typo.
allow \# in chrom name, just not at beg. of line (header)
Allow user to force closest interval to have different name (-N)
added -A option to subtract entire interval when any overlap
added shuffle logic for BEDPE
no need for flanks to the left of chrom.start
reset each bedpe
slightly better randomization
first cut at sphinx-based docs
added docs/_build. working on plots via @daler
include html
intersect docs
add plotting to conf.py
remove redundancy in conf.py
trying to suppor mpl
trying to suppor mpl
add pip reqs. in hopes of mpl support on rtd
add pip reqs. in hopes of mpl support on rtd
add setup.py. for venv
reorg for rtd
numpy for rtd
numpy for rtd
numpy for rtd
numpy for rtd
use correct Makefile
fix flanks for zerlonegth features.
typo in closest help
added -split, -s, -S, -f, -r support to multicov
menu typo
try Mock()
try Mock()
no need for setup.py?
add plot_directive
add pybedtools req. for docs
try reqs file
extraneous tab for windowbed -c
remove comment
send warning to stderr.
complement warns to stderr.
fix corner case in chrom sweep. addresses GC issue #141
exit is inout BAM file is not found
standardize tag reporting for bamtobed
clear closest list if an overlap in closest
80char cleanup of merge.
Prefer list over vector chromsweep's cache. Huge performance increases
missing include
support for extracting blocked BED records in fastaFromBed
tweak healp for -split. cheers to @brentp for the nice addition
formatting
avoid -hist overflow
80 char width
80 char width
80 char width
refactor VCF auto-detection
80 char
add "first" and "last" as new groupby options
added new jaccard tool. see PMID: 22693437
jaccard tests
Setting Release-Version v2.17.0
update HISTORY
Merge branch 'master' of github.com:arq5x/bedtools
[BUG] fix jaccard regression test.
[NEW] Added new "reldist" tool to measure the distribution of relative distances between two files
[OMM] add reldist source...
[BUG] non-redundant cluster ids in stranded (-s) mode.
[BUG] closest -s fails to report when only opp. strand B ivls exists.
[ENH] improve desc. of what -wb does.
[ENH] Make it more clear than -abam supplants -a
first cut at allowing -incl and -excl
allow -incl and -excl
remove commented code
update .gitignore
[ENC] Add -N (removeAny) option to subtract. Re-adding improvement from @brentp
[DOCS] updated sphinx docs for intersect.
[DOCS] updated sphinx docs for groupby
[DOCS] updated version.
[DOCS] update groupby usage
[BUG] typo in database length calc.
Merge branch 'master' of github.com:arq5x/bedtools
restructure docs
[DOCS] update sphinx docs for annotate
[ENH] user controls MAX_TRIES (-maxTries) in shuffle.
[DOCS] add sphinx docs for shuffle
[ENH] jaccard now works in a single pass.
[TST] new tests for Jaccard
[BUG] Removed unnecessary pointer deletion in tag's destructor. Cheers to @yarden and @jmarshall.
[BUG] Fix regression in reporting all overlapping features for . Thanks to @jsilter.
[ENH] Properly handle empty, yet existent files. Thanks to @jpaulLD and @jmarshall.
[DOCS] Add Disqus and Github editing to docs. Cheers to @ctb
cleanup conf.py
[DOC] Typo and path error in page.html
[ENH] support MS Windows line endings (\r\n). Output is always \n
Merge branch 'master' of github.com:arq5x/bedtools
[DOCS] updates to annotate, bamtobed, and multicov
[DOCS] ommission in multicov
[TST] fix jaccard test for stdin
[DOCS] new docs for bamtofastq
[DOCS] multiple improvements to HTML docs
add unstaged files
[DOCS] update adv usage.
update FAQ
[DOCS] several improvements to docs
added RetroSeq to Related Tools.
[DOCS] remove superfluous section labels
[DOC] add docs for bedtools map
tweaks to map docs
lower res image
[DOCS] update maskfasta docs
[DOCS] updates to intersect and subtract docs.
[DOCS] updates to intersect and subtract docs.
[DOCS] update window docs
[DOCS] updated slop docs
[DOC] prefer :doc: directive for internal links
[DOC] update docs for shuffle.
[DOC] update merge docs.
[DOC] update docs for merge and cluster
[DOC] tweak cluster glyph
[DOCS] update getfasta docs.
[DOC] new docs for random
[DOC] update complement docs
[DOCS] multiple tweaks.
[DOC] add docs for flank.
update FAQ
[DOC] updated genomecov docs
[DOC] add link Biostar queries.
[EHN] add -delim option to bedtools merge
[DOC] update merge docs
[DOC] update groupby docs. Thanks to @brentp
Merge branch 'master' of github.com:arq5x/bedtools
report which chrom can't be found in -incl
Merge branch 'master' of github.com:arq5x/bedtools
[DOC] update FAQ regarding zlib compilation issues.
[ENH] add -mate1 option for -bedpe output in bamtobed
Merge branch 'master' of github.com:arq5x/bedtools
[DOC] add docs for the -noOverlapping option in shuffle.
[BUG] -split, -tag and BED6 output was not implemented.
Aaron Quinlan (185):
Initial BEDTools Commit
Changed bedFile.cpp to allow input from stdin for the unbinned BED Map.
Added the obj directory
coverageBed.cpp:
Changed all of the Makefiles to only write the binary to bin/
Added master makefile to compile all programs in the BEDTools project
New algorithm and bug fixes for genomeCoverageBed
Changed exception handling calls to report errors to stderr.
Updated mergeBed reporting logic
Updated bedFile.cpp for better stdin support
Changed usage statements to include infor on stdin
Updated complemeMentMain usage to include stdin example.
Added writeA (-wa) parameter to intersectBed
Changed the usage banner on all programs to be less showy
Added new windowBed program
Updated usage statement for windowBed.
Update "master" Makefile to include windowBed
First public source release. Version 1.1
Updated README and USAGE_EXAMPLES
Updated README to acknowledge Galaxy
Added VERSION and spruced up USAGE_EXAMPLES
Updated includes to ease compilation on other systems.
Added closestBed
Updated bedFile.cpp and bedFile.h
Updated atomic Makefiles to include "-Wall". Updated master Makefile to include closestBed
Removed unused variable "slop" from cloestMain.cpp
Updated code to address warnings from -Wall
Improved the usage statements in *Main.cpp
Added additional sorting options to sortBed
Added subtractBed
Added linksBed and updated Makefile
Update master Makefile
Updated sortMain.cpp to force -i stdin
Version 1.2. Added closestBed, linksBed and subtractBed
Updated README.
Added tracking to bin/ and obj/
Updated README...again.
Updated README
Updated README for the millionth time.
Updated README: typos
Updated README (typos) and added FAQ
Updated README (typos)
Updated TODO
Updated copyright in USAGE_EXAMPLES
Strandedness. reportBed in bedFile. peIntersect
Merge pull request #7 from daler/master
Merge pull request #8 from daler/master
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Update BlockMgr.cpp
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Update README.md
Update conf.py
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Merge pull request #410 from rishavray/feature/#406getfasta
Merge pull request #404 from jmarshall/fix-GetNextBed
Aaron R. Quinlan (1):
add missing include to prevent compilation error
Alex Penson (2):
Update advanced-usage.rst
Update installation.rst
Andreas Tille (4):
Imported Upstream version 2.20.1
Merge branch 'master' of ssh://git.debian.org/git/debian-med/bedtools
Merge https://github.com/arq5x/bedtools2
Imported Upstream version 2.26.0+dfsg
Andrey Kartashov (4):
BAM files, genomecov pair-end fragment size, or fixedFragment size -pc -fs
BUG Fix
Check if right side goes below 0
Documentation added - corrected binding for start end
Arjan van der Velde (1):
changed compare function to have "unsigned int"
Assaf Gordon (12):
WindowMaker: add output ID option.
WindowMaker: fix bug with fixed number of windows.
Makefile: Auto-generate version string from Git version
Restructure auto-git-version
Makefile: add DEBUG compiler option.
Makefile: extract the sub-dir make into targets.
Makefile: extract BamTools' API creating to a separate target.
Second attemp at automatic versioning system.
autoversion: fix typo in git directory name
auto-version: fix missing git detection
WindowMaker: bugfix with using "srcwinnum" + genome
BamToBed: properly fail on non-existing input files.
Avinash Ramu (1):
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