1. 26 Apr, 2010 6 commits
  2. 22 Apr, 2010 2 commits
    • Aaron's avatar
      Added NULL terminator to AddBamTag() in BamAux.h · 5c5b74b4
      Aaron authored
      5c5b74b4
    • Aaron's avatar
      Several changes: · 628eff12
      Aaron authored
      	1. Added an enum for BED line status in an effort to handle
                 header and blank lines in an input file.
      	2. Modified the Open/Get/Close idiom to only test against
                 BED_INVALID status.  Only intersectBed and bedFile.cpp
                 were updated.
      	3. Added AddBamTag to BaumAux.h
      	4. Wrote bamFillMateSeq
      628eff12
  3. 15 Apr, 2010 8 commits
  4. 14 Apr, 2010 2 commits
  5. 12 Apr, 2010 1 commit
    • Aaron's avatar
      Added the -wao option to intersectBed. · 27234494
      Aaron authored
      	- Allows one to report 0 overlap for non-overlapping A features
      	- Changed all private memeber variables to use "_VAR" notation.
      	- Added convenience functions for reporting overlaps.
      27234494
  6. 29 Mar, 2010 1 commit
  7. 24 Mar, 2010 2 commits
  8. 23 Mar, 2010 7 commits
  9. 22 Mar, 2010 2 commits
  10. 19 Mar, 2010 1 commit
  11. 18 Mar, 2010 5 commits
  12. 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
  13. 15 Mar, 2010 2 commits