1. 18 Jul, 2010 2 commits
  2. 17 Jul, 2010 1 commit
  3. 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
  4. 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
  5. 26 Apr, 2010 1 commit
  6. 15 Apr, 2010 1 commit
  7. 18 Mar, 2010 1 commit
  8. 05 Jan, 2010 1 commit
  9. 04 Jan, 2010 1 commit
  10. 05 May, 2009 2 commits
  11. 26 Apr, 2009 1 commit
  12. 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
  13. 23 Apr, 2009 1 commit
  14. 10 Apr, 2009 1 commit
  15. 09 Apr, 2009 1 commit