[med-svn] [bedtools] annotated tag debian/2.19.0-1 created (now 0e33a1b)

Charles Plessy plessy at moszumanska.debian.org
Sun Feb 16 07:21:58 UTC 2014


This is an automated email from the git hooks/post-receive script.

plessy pushed a change to annotated tag debian/2.19.0-1
in repository bedtools.

        at  0e33a1b   (tag)
   tagging  f93eb83fe32cf4a14db35a63542c4772dba31013 (commit)
  replaces  debian/2.17.0-1
 tagged by  Charles Plessy
        on  Sun Feb 16 16:21:02 2014 +0900

- Log -----------------------------------------------------------------
bedtools (2.19.0-1) unstable; urgency=low

  e07e70c Imported Upstream version 2.19.0
  afdc61a Watch GitHub at https://github.com/arq5x/bedtools2.
  4abe14e Source control file normalised with config-model-edit.
  0518353 Corrected a typo in the long description. (Closes: #714873)
  f63d85e Follow the layout of the upstream repository.
  c25f9e5 Correct name of README file in debian/docs.
  5561c7c Emulate source format 1.0 in the format 3.0 (quilt).
  a45a0ab Canonical VCS URLs.
  4459dfe Conforms with Policy 3.9.5.

 -- Charles Plessy <plessy at debian.org>  Sat, 15 Feb 2014 19:39:23 +0900
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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 (95):
      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
      Merge pull request #9 from jakebiesinger/master
      Merge pull request #13 from jakebiesinger/master
      Merge pull request #14 from jakebiesinger/master
      Merge pull request #15 from agordon/feature/makewindows_with_IDs1
      Merge pull request #16 from agordon/feature/auto_git_version
      Merge pull request #17 from agordon/feature/minimal_version_recompile
      Merge pull request #18 from agordon/feature/makefile_debug
      Merge pull request #20 from agordon/feature/makewindows_name_fix
      Merge pull request #22 from agordon/bugfix/bamtobed_non_existing_file
      Merge pull request #25 from brentp/groupby-columns
      Merge pull request #26 from brentp/groupby_header
      Merge pull request #27 from nathanweeks/master
      Merge pull request #28 from brentp/getfasta
      Merge pull request #29 from charles-plessy/master
      Merge pull request #45 from pryvkin/master
      Update docs/index.rst
      Update docs/index.rst
      Merge pull request #52 from jmarshall/build-infrastructure
      Merge pull request #54 from brentp/jaccard_n
      Merge pull request #58 from dvanic/patch-1
      Merge pull request #59 from cdelzinga/patch-1
      Merge pull request #60 from lbthrice/patch-1
      Merge pull request #62 from xubeisi/patch-1
      Merge pull request #64 from alexpenson/patch-1
      Merge pull request #75 from lbthrice/patch-2
      Merge pull request #76 from brentp/no-overlap
      Merge pull request #79 from nachocab/patch-1
      Merge pull request #81 from daler/patch-2
      Merge pull request #80 from daler/patch-1
      Merge pull request #82 from wac/patch-1
      Merge pull request #4 from nkindlon/master
      Merge pull request #5 from nkindlon/master
      Merge pull request #6 from nkindlon/master
      Merge pull request #7 from nkindlon/master
      Merge pull request #14 from nkindlon/master
      Update README.rst
      Merge pull request #15 from nkindlon/master
      Update README.rst
      Merge pull request #20 from nkindlon/master
      Update cluster.rst
      Merge pull request #25 from nkindlon/master
      Merge pull request #31 from timflutre/master
      Merge pull request #32 from timflutre/master
      Merge pull request #33 from nkindlon/master
      Merge pull request #35 from jayhesselberth/intersphinx
      Merge pull request #36 from arjanvandervelde/patch-1
      Merge pull request #37 from jayhesselberth/patch-1
      Update README.md

Aaron R. Quinlan (1):
      add missing include to prevent compilation error

Alex Penson (1):
      Update advanced-usage.rst

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.

Brent Pedersen (11):
      add TokenizeColumns function
      use TokenizeColumns in groupBy and add lineFileUtilities as dependency to Makefile
      add tests for groupby
      let groupby handle a header line (starting with "#") as do other
      start of allowing to get concatenated sequence of exons
      errant debug
      start of test for -exons arg
      change -exons to -split. add tests that make sense.
      allow - to be specified for stdout fasta
      add n_intersections to jaccard output
      ENH: shuffle intervals to non-overlapping locations.

Charles Plessy (19):
      Call bedtools via a shell variable called BT.
      Allow overriding BT to test bedtools from other paths.
      Source control file normalised with config-model-edit.
      Corrected a typo in the long description.
      Work in progress.
      Watch GitHub at https://github.com/arq5x/bedtools2.
      Work in progress.
      Imported Upstream version 2.19.0
      Merge tag 'upstream/2.19.0'
      New upstream releases; no new copyright nor license notice.
      Merge branch 'master' into debian/unstable
      Follow the layout of the upstream repository.
      Moved to GitHub.
      README file changed format.
      Emulate source format 1.0 in the format 3.0 (quilt).
      Canonical VCS URLs.
      Conforms with Policy 3.9.5.
      Merge branch 'master' into debian/unstable
      bedtools (2.19.0-1) unstable; urgency=low

Jake Biesinger (7):
      Added a signed distance option (-D) to closestBed
      Fix typo in closestBed: -S for opposite strands, not -s
      Oops.  Extra ;
      User can specify one of three orientations (a,b,ref)
      Add ignore options for features up- and down-stream of A
      Bugfix: fix segfault when -t first or -t last used with -iu or -id
      Fix regression on intersectBed -wao, now reports all features from A,

Jay Hesselberth (1):
      Update related-tools.rst

John Marshall (2):
      Ignore generated source files and library
      Build these objects only once

Nacho Caballero (1):
      Change the actual default delim for merge (it's ";" not ",")

Nathan Weeks (2):
      sockaddr_in and sockaddr_in6 are defined in netinet/in.h, which may or may not be included by arpa/inet.h (per POSIX.1-2008). Explicitly include netinet/in.h to compilation on FreeBSD 9.0.
      If "tac" doesn't exist (e.g., on non GNU/Linux systems like OS X & other BSDs), emulate with sed '1!G;h;$!d' (from http://www.catonmat.net/blog/sed-one-liners-explained-part-one/)

Paul Ryvkin (1):
      Fixed segfault with -names option in tagBam

Ryan Dale (2):
      Update quick-start.rst
      Update quick-start.rst

Timothee Flutre (2):
      add files to test getfasta with full header
      add option -fullHeader for fasta files

Timothée Flutre (1):
      typo on option -useFullHeader

Warren Cheung (1):
      Update slop.rst

arjanvandervelde (1):
      Update installation.rst

arq5x (72):
      [TST] resolve platform-specific issues with GNU cut.
      [TST] tests for reldist
      Add sample to main menu
      [ENH] add -allowBeyondChromEnd feature to shuffle.
      sync docs
      [TST] cleanup sample test
      [BUG] case typo that OSX tolerated.
      [BUG] case typo that OSX tolerated.
      [ENH] intergrate merge changes from @kcha.
      [DOC] update docs for new -g option in intersect for specifying custom sort order.
      [DOC] add docs for the jaccard tool.
      [DOC] tweak intersect usage doc
      [DOC] docs for the reldist tool.
      update README
      update README
      update README
      typo
      Setting Release-Version v2.18.0
      Setting Release-Version v2.18.0
      Setting Release-Version 2.18.0
      bump docs to 2.18.0
      tweak logo
      Setting Release-Version v2.18.0
      [DOC] tweak intersect docs
      [DOC] update release history and subtract's docs
      Setting Release-Version v2.18.0
      [DOC] fix subtract's option list:
      add citations
      [BUG] fix compilation errors on CLANG and with pre-installed bamtools libs.
      Setting Release-Version v2.18.1
      [DOC] fix docs typos
      [DOC] cleanup docs to facilitate man page creation.
      add travis config
      tweak travis config
      ask travis to auto-run unit tests.
      Setting Release-Version v2.18.2
      [BUG] fix extra TAB at EOL in the annotate tool.
      Merge branch 'master' of https://github.com/arq5x/bedtools2
      [TST] new unit tests for proper field reporting for BED* intersections
      tweak
      first pass at using Context and PFM for the map tool.
      [TST] add new tests for map
      [ENH] add absmin and absmax to VectorOps and map tool.
      [BUG] change getField() logic in GffRecord
      [ENH] add str() method to QuickString
      formatting
      map uses PFM.
      add nullValue and ColOp to ContextBase for Map
      allow RecordOutputMgr to print a record followed by arbitray string
      add methods to extract column from record by its col. number
      add methods to extract column from record by its col. number (2)
      add a Context for Map tool.
      reduce QuickString DEFAULT_CAPACITY to 8 instead of 256 to save memory.
      fix conflict
      fix conflict.
      fix conflict.
      [TST] add tests for map
      [ENH] add test when -fullHeader not provided
      [ENH] correct Jaccard output header
      fix bug in merge output and cleanup jaccard test
      [DOC] add speed comparo to docs
      add speed comparo to README
      tweaks
      tweaks
      typo.
      add -valueOnly option to jaccard
      update map docs
      update sidebar
      add intersphinx support thanks to @jayhesselberth
      Setting Release-Version v2.19.0
      Setting Release-Version v2.19.0
      Setting Release-Version v2.19.0

cdelzinga (1):
      Update coverage.rst

daler (2):
      include cstdlib for gcc 4.4.3
      windowBed -sm -> -Sm

dvanic (1):
      removed duplicate description of -s option

jayhesselberth (2):
      * modified rst to add labels for inclusion in objects.inv & intersphinx
      * fix spelling

lbthrice (2):
      Update sort.rst
      Update merge.rst

nkindlon (58):
      First commit for new 2.18-alpha branch.
      forgot intersectFile
      added other util directories
      added more utils
      added sandbox and regressTest
      Corrected intersect showHelp segfault.
      -g (genomeFile) option now gives error if file is differently sorted than genome file.
      resolved chromId problem when doing Chromsweep with BAM file sorted differently than genome file.
      fixed negative coords, zero len intervals, Bed4 format error
      Improved help and error msgs in Context
      Merge pull request #1 from arq5x/master
      handling for unmapped Bam records
      Shortened output buffer, corrected Chromsweep errors with some print options due to early termination.
      Added -g option and descriptor to intersect help message.
      Fixed chromId bug, removed debug metric from RecordOutputMgr
      Fixed unmapped mate bug
      added BamRecord::printUnmapped method for noHit and count functionality.
      Moved short circuit for BAM unmapped reads to Record::sameChromIntersect for when query record isn't BAM but DB record is.
      Stopped BinTree from loading or getting hits for unmapped reads.
      added fifo handling
      Added support for Bgzip from files and stdin.
      Fixed test for Bam vs Bgzip to allow for empty references.
      Fixed small memory leak in InputStreamMgr.
      new unit tests for intersect
      Fixed a bug in BamRecord::printUnmapped, added a unit test with with data file for unmapped Bam reads.
      added unit tests and data file for sort order, genome file, and more Bam unmapped reads.
      Added more unit tests for bed, gzip, and bgzipped files with large headers from file, redirect, pipe and fifo.
      Added 12 new tests to print header for files with large header from uncompressed files, gzip, and bgzip as file, redirect, pipe and fifo.
      New unit tests for sort order enforcement, non-existant file. Also added performance test for file input and compression types.
      Added unit test and changed error message for empty files.
      Added unit test for unrecognized arguments.
      Added sample sub-program with needed changes to main, Makefiles, Context, FileRecordMgr, and RecordOutputMgr.
      Added unit tests for sampleFile program.
      Fixed sample and intersect unit tests; minor code changes; new repository.
      Actually needed j1.bed in test/intersect.
      ifdef'd out DualQueue and removed usages of it to fix compiler errors with clang on Mac OS X
      Changed main Makefile to put LDFLAGS after -lbamtools. Fixes customized Bamtools link error when Bamtools already defined in /usr/lib.
      Changed input stream buffer to only 1Kb to improve performance for small files.
      Corrected comment and constant for MAIN_BUF_READ_SIZE.
      Changed outbuf size constant to 16384 from 16386, which was a mistake.
      Added -nobuf option, and changed flush to occur after every record if -nobuf is set.
      Added -nobuf option and definition to intersect help menu.
      Added fix for Bam files with empty headers. Added test for this to unit test.
      Refactored Context class into Base and Derived classes for cleaner future development.
      Changed handling of strand in records to allow non-strand strings in sixth field of records.
      Merge remote-tracking branch 'upstream/master'
      Merge remote-tracking branch 'upstream/master'
      Fixed split bug, added field number accessibility.
      New unit test for -split -wo
      Added another file to intersect unit tests for split blocks testing.
      Corrections and unit tests for split bug.
      Forgot new file for unit tests
      Refactored contexts for validation, added unit tests, enabled -plit for map.
      Fixed a cut/paste error in unit test comment.
      Removed outdated comment
      Removed unnecessary NULL checks on delete.
      Added unit test to intersect for gff files.
      Added -split option to map help.

xubeisi (1):
      Update coverage.rst

“arq5x” (1):
      Added version.h to simplify versioning

-----------------------------------------------------------------------

This annotated tag includes the following new commits:

       new  1ba07ad   Update related-tools.rst
       new  2039594   Merge pull request #37 from jayhesselberth/patch-1
       new  c8bfb02   Update README.md
       new  c25f9e5   README file changed format.
       new  5561c7c   Emulate source format 1.0 in the format 3.0 (quilt).
       new  a45a0ab   Canonical VCS URLs.
       new  4459dfe   Conforms with Policy 3.9.5.
       new  39c861d   Merge branch 'master' into debian/unstable
       new  f93eb83   bedtools (2.19.0-1) unstable; urgency=low

The 9 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.


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