1. 01 Jul, 2010 2 commits
  2. 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
  3. 15 Apr, 2010 1 commit
  4. 24 Mar, 2010 1 commit
  5. 18 Mar, 2010 1 commit
  6. 04 Jan, 2010 2 commits
  7. 18 Nov, 2009 1 commit
  8. 16 Nov, 2009 1 commit
  9. 11 May, 2009 1 commit
  10. 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
  11. 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
  12. 26 Apr, 2009 3 commits
  13. 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
  14. 23 Apr, 2009 1 commit
  15. 10 Apr, 2009 1 commit