1. 03 Jan, 2011 1 commit
  2. 22 Sep, 2010 1 commit
  3. 21 Sep, 2010 1 commit
  4. 18 Aug, 2010 1 commit
    • Aaron's avatar
      Big commit. · b9ab28d0
      Aaron authored
      	1. Added new version of BamTools supporting uncompressed BAM.
      	2. Added -ubam option to intersectBed.
      	3. First functional release of annotateBed.
      	4. Updated GetEditDistance calls to GetTag(NM) per the new API change in BamTools.
      b9ab28d0
  5. 18 Jul, 2010 1 commit
  6. 15 Apr, 2010 2 commits
  7. 29 Mar, 2010 1 commit
  8. 23 Mar, 2010 1 commit
  9. 17 Mar, 2010 1 commit
    • Aaron's avatar
      Improvements to coverageBed · f733cafd
      Aaron authored
      	1. Added the -hist option (credit to Jose Bras).
      	2. Substantially improved the speed by using a depth iterator instead of copying the depth map for each feature in B when computing coverage.
      f733cafd
  10. 23 Jan, 2010 1 commit
  11. 04 Jan, 2010 1 commit
  12. 03 Jan, 2010 1 commit
  13. 01 Jan, 2010 1 commit
  14. 30 Dec, 2009 2 commits
    • Aaron's avatar
      Updated genomeCoverageBed. · 4ff410b4
      Aaron authored
      	1. Revised usage to 80 chars
      	2. GPL headers
      	3. Added new stdin logic
      	4. Changes logo.
      	5. Revised the usage statement.
      4ff410b4
    • Aaron's avatar
      Updated coverageBed and bedFile.cpp · d9fcb67c
      Aaron authored
      	1. Revised usage to 80 chars
      	2. GPL headers
      	3. Added new stdin logic
      	4. Changes logo.
      	5. Updated bedFile.cpp's loadBedIntoMapBin to support stdin.
      d9fcb67c
  15. 18 Nov, 2009 1 commit
  16. 27 Oct, 2009 1 commit
    • Aaron's avatar
      Version 2.2.4 (10/27/2009) · 885b0515
      Aaron authored
      	1. Updated the mergeBed documentation to describe the -names option which allows one to report the names of the
      	features that were merged (separated by semicolons).
      885b0515
  17. 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
  18. 15 Jun, 2009 1 commit
    • Aaron's avatar
      VERSION 2.1.0 · 23c77070
      Aaron authored
      	1. Fixed a bug in peIntersectBed that prevented -a from being correctly handled when passed via stdin.
      	2. Added new functionality to coverageBed that calculates the density of coverage.
      	3. Fixed bug in genomeCoverageBed.
      23c77070
  19. 12 May, 2009 1 commit
  20. 05 May, 2009 1 commit
  21. 27 Apr, 2009 1 commit
    • Aaron Quinlan's avatar
      Version 1.2. Added closestBed, linksBed and subtractBed · a1af7c6a
      Aaron Quinlan authored
      	1.  Added subtractBed.
      		A. Fixed bug that prevented "split" overlaps from being reported.
      		B. Prevented A from being reported if >=1 feature in B completely spans it.
      	2.  Added linksBed.
      	3.  Added the ability to define separate windows for upstream and downstream to windowBed.
      a1af7c6a
  22. 26 Apr, 2009 1 commit
  23. 24 Apr, 2009 1 commit
    • Aaron Quinlan's avatar
      First public source release. Version 1.1 · ff4edaf0
      Aaron Quinlan authored
      	1.  Added a README for installation
      	2.  Modified intersectBed and windowBed to call one function for
      	    finding overlaps.  This function is now called when reading
      	    from cin or from a file.
      	3.  Added acknowledgements.
      	4.  Corrected the PROGRAM_NAME in coverageBed
      ff4edaf0
  24. 23 Apr, 2009 1 commit
  25. 15 Apr, 2009 1 commit
  26. 10 Apr, 2009 1 commit
    • Aaron Quinlan's avatar
      coverageBed.cpp: · 319d42fd
      Aaron Quinlan authored
      	Changed the include from graphBed.h to coverageBed.h
      coverageMain.cpp:
              Changed the include from graphBed.h to coverageBed.h
      319d42fd
  27. 09 Apr, 2009 1 commit