1. 28 May, 2015 3 commits
  2. 18 Sep, 2014 1 commit
  3. 24 May, 2014 1 commit
  4. 23 May, 2014 2 commits
  5. 17 Dec, 2013 1 commit
  6. 13 Dec, 2013 1 commit
  7. 03 Nov, 2012 1 commit
  8. 03 Nov, 2011 3 commits
  9. 26 Oct, 2011 1 commit
  10. 30 Sep, 2011 1 commit
  11. 23 Sep, 2011 1 commit
  12. 07 Sep, 2011 1 commit
  13. 04 Apr, 2011 1 commit
  14. 31 Jan, 2011 1 commit
  15. 21 Jan, 2011 1 commit
  16. 22 Sep, 2010 1 commit
  17. 16 Aug, 2010 1 commit
  18. 26 Jul, 2010 1 commit
  19. 18 Jul, 2010 1 commit
  20. 06 Jul, 2010 1 commit
  21. 05 Jul, 2010 1 commit
  22. 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
  23. 06 May, 2010 1 commit
  24. 05 May, 2010 1 commit
  25. 29 Mar, 2010 1 commit
  26. 24 Mar, 2010 1 commit
  27. 23 Mar, 2010 1 commit
  28. 10 Mar, 2010 1 commit
  29. 19 Feb, 2010 1 commit
    • Aaron's avatar
      Version 2.5.3 (Feb-19-2010) · 19a7d197
      Aaron authored
      	1. Fixed bug to "re-allow" track and "browser" lines.
      	2. Fixed bug in reporting BEDPE overlaps.
      	3. Fixed bug when using type "notboth" with BAM files in pairToBed.
      	4. When comparing BAM files to BED/GFF annotations with intersectBed or pairToBed, the __aligned__ sequence is used, rather than the __original__ sequence.
      	5. Greatly increased the speed of pairToBed when using BAM alignments.
      	6. Fixed a bug in bamToBed when reporting edit distance from certain aligners.
      19a7d197
  30. 03 Feb, 2010 1 commit
    • Aaron's avatar
      Version 2.5.2 (Feb-2-2010) · e5007f9c
      Aaron authored
      	1. The start and end coordinates for BED and BEDPE entries created by bamToBed are now based on the __aligned__ sequence, rather than the original sequence.  It's obvious, but I missed it originally...sorry.
      	2. Fixed a bug in bamToBed that caused a crash when created BED / BEDPE from "spliced" BAM alignments.
      	3. Added an error message to mergeBed preventing one from using "-n" and "-nms" together.
      	4. Fixed a bug in pairToBed that caused neither -type "notispan" nor "notospan" to behave as described.
      e5007f9c
  31. 28 Jan, 2010 2 commits
    • Aaron's avatar
      Fixed line parsing bug. · 8c0df1a3
      Aaron authored
      	1. atoi fails in parseLine when start = 0.  Changed to strtol.
      	2. modified parseBedLine and parseGffLine to do better sanity checking.
      8c0df1a3
    • Aaron's avatar
      Version 2.5.0 · e186bcbf
      Aaron authored
      e186bcbf
  32. 23 Jan, 2010 1 commit
  33. 11 Jan, 2010 1 commit
  34. 10 Jan, 2010 1 commit