1. 24 Jan, 2012 2 commits
  2. 08 Jan, 2012 1 commit
  3. 08 Dec, 2011 2 commits
  4. 29 Nov, 2011 1 commit
  5. 01 Nov, 2011 2 commits
  6. 25 Oct, 2011 2 commits
  7. 31 Aug, 2011 1 commit
  8. 14 Jun, 2011 1 commit
  9. 03 Mar, 2011 1 commit
  10. 03 Jan, 2011 1 commit
  11. 22 Sep, 2010 1 commit
  12. 06 Aug, 2010 2 commits
  13. 04 Aug, 2010 2 commits
  14. 18 Jul, 2010 1 commit
  15. 29 Jun, 2010 1 commit
    • Aaron's avatar
      Large commit · ff07e83c
      Aaron authored
      	1. Reset BED.strand to be string instead of char in the interest of generality.
      	2. Fixed bug in genomeCoverageBed where NULL entries where genome summaries were err. reported with -bga.
      	3. Fixed bug in closestBed where NULL entries were err. reported when BED > 6.
      	4. Standardized the Open, Get, Close idiom per improvements from Gordon Assaf.
      	5. Add "split" logic to bamToBed.
      ff07e83c
  16. 06 May, 2010 1 commit
  17. 26 Apr, 2010 1 commit
  18. 15 Apr, 2010 2 commits
  19. 03 Jan, 2010 1 commit
  20. 01 Jan, 2010 2 commits
  21. 29 Dec, 2009 1 commit
    • Aaron's avatar
      Updated closestBed · ad9419b0
      Aaron authored
      	1. Revised usage to 80 chars
      	2. GPL headers
      	3. Added new stdin logic
      ad9419b0
  22. 19 Nov, 2009 2 commits
  23. 16 Nov, 2009 1 commit
  24. 15 Oct, 2009 1 commit
  25. 18 Sep, 2009 1 commit
    • Aaron's avatar
      Version 2.2.0 · 952c45ad
      Aaron authored
      === Notable changes in this release ===
      1.  coverageBed will optionally only count features in BED file A (e.g. sequencing reads) that overlap with
      	the intervals/windows in BED file B.  This has been requested several times recently and facilitates CHiP-Seq and
      	RNA-Seq experiments.
      
      2.  intersectBed can now require a minimum __reciprocal__ overlap between intervals in BED A and BED B.  For example,
      	previously, if one used -f 0.90, it required that a feature in B overlap 90% of the feature in A for the "hit"
      	to be reported.  If one adds the -r (reciprocal) option, the hit must also cover 90% of the feature in B.  This helps
      	to exclude overlaps between say small features in A and large features in B:
      
      	A ==========
      	B  **********************************************************
      
      	-f 0.50 (Reported), whereas -f 0.50 -r (Not reported)
      
      3.  The score field has been changed to be a string.  While this deviates from the UCSC definition, it allows one to track
      	much more meaningful information about a feature/interval.  For example, score could now be:
      
      	7.31E-05  (a p-value)
      	0.334577  (mean enrichment)
      	2:2.2:40:2 (several values encoded in a string)
      
      4.  closestBed now, by default, reports __all__ intervals in B that overlap equally with an interval in A.  Previously, it
      	merely reported the first such feature that appeared in B.  Here's a cartoon explaining the difference.
      
      	**Prior behavior**
      
      	A	 ==============
      	B.1        				++++++++++++++
      	B.2       				++++++++++++++
      	B.3               				+++++++++
      
      	-----------------------------------------
      	Result = B.1 			++++++++++++++
      
      	**Current behavior**
      
      	A	 ==============
      	B.1        				++++++++++++++
      	B.2       				++++++++++++++
      	B.3               				+++++++++
      
      	-----------------------------------------
      	Result = B.1 			++++++++++++++
      			 B.2 			++++++++++++++
      
      	Using the -t option, one can also choose to report either the first or the last entry in B in the event of a tie.
      
      5.  Several other minor changes to the algorithms have been made to increase speed a bit.
      952c45ad
  26. 17 Sep, 2009 1 commit
    • Aaron's avatar
      VERSION 2.1.2 · 572c76e0
      Aaron authored
      1. Fixed yet another bug in the parsing of "track" or "browser" lines.  Sigh...
      2. Change the "score" column (i.e. column 5) to b stored as a string.  While this deviates
         from the UCSC convention, it allows significantly more information to be packed into the column.
      572c76e0
  27. 19 May, 2009 1 commit
  28. 05 May, 2009 1 commit
    • Aaron Quinlan's avatar
      Strandedness. reportBed in bedFile. peIntersect · ac52b452
      Aaron Quinlan authored
      	1. Added strandedness to relevant programs (e.g. intersectBed, mergeBed, etc.)
      	2. Moved reportBed and reportBedRange to bedFile.cpp to clean up code
      	3. Sped up file parsing.  Added lineFileUtilities.cpp
      	4. Added peIntersectBed
      ac52b452
  29. 26 Apr, 2009 2 commits