1. 14 Jan, 2011 1 commit
  2. 03 Jan, 2011 3 commits
  3. 22 Sep, 2010 1 commit
  4. 21 Sep, 2010 1 commit
  5. 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
  6. 16 Aug, 2010 2 commits
  7. 04 Aug, 2010 1 commit
    • Aaron's avatar
      Multiple changes. · 5d8e5739
      Aaron authored
      	1. Fixed bug where an extra tab is inserted prior to \n in the report*Newline methods.
      	2. Fixed bug causing incorrect behavior when first bed feature has stant and end = 0.
      5d8e5739
  8. 18 Jul, 2010 1 commit
  9. 17 Jul, 2010 1 commit
  10. 06 Jul, 2010 1 commit
  11. 05 Jul, 2010 1 commit
  12. 04 Jul, 2010 1 commit
    • Aaron's avatar
      Large commit. · 3cba5c6c
      Aaron authored
      	A. Fixed massive bug in parseBedLine that disallowed BED features with start = 0.  Bad news.
      	1. Moved ToString to lineFileUtilities
      	2. Added tabFile class.  Works with gzip as well.
      	3. Changed groupBy to use the new TabFile class.
      	4. Added new collapse feature to groupBy.
      3cba5c6c
  13. 01 Jul, 2010 2 commits
  14. 30 Jun, 2010 1 commit
    • Aaron's avatar
      Multiple changes. · 184656c1
      Aaron authored
      	1.  Added support for VCF 4.0.  BED.end is based on the size of the REF allele in the VCF entry.
      	2.  Fixed a bug in BamReader.cpp that bombed when seq and qual are == "*"
      	3.  Changed the Makefiles to inherit flags from the master Makefile in the root directory.
      	4.  Fixed a bug in bedToBam to created incorrect CIGAR strings for the first block.
      184656c1
  15. 15 Apr, 2010 1 commit
  16. 24 Mar, 2010 1 commit
  17. 18 Mar, 2010 1 commit
  18. 04 Jan, 2010 2 commits
  19. 18 Nov, 2009 1 commit
  20. 16 Nov, 2009 1 commit
  21. 11 May, 2009 1 commit
  22. 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
  23. 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
  24. 26 Apr, 2009 3 commits
  25. 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
  26. 23 Apr, 2009 1 commit
  27. 10 Apr, 2009 1 commit