1. 29 Jun, 2010 2 commits
    • Aaron's avatar
    • 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
  2. 08 Jun, 2010 1 commit
  3. 07 Jun, 2010 2 commits
    • Aaron's avatar
      Added gzstream to master branch · 791e6564
      Aaron authored
      791e6564
    • Aaron's avatar
      Large, performance-related commit. · f792d8eb
      Aaron authored
      	1. Created separate structs for BED and BEDCOV in order to reduce memory consumption.  Savings of ~30%.
      	2. Changed the binning approach to make 16kb bins the most granular.  IntersectBed is now 1/3 faster as a result.
      	3. Templated the parsing and reporting functions in bedFile.  Had to move them to the header file to avoid linker complications.
      	4. Added CHRPOS as a common type.
      f792d8eb
  4. 06 May, 2010 2 commits
  5. 05 May, 2010 5 commits
  6. 04 May, 2010 3 commits
  7. 03 May, 2010 2 commits
  8. 29 Apr, 2010 4 commits
  9. 26 Apr, 2010 6 commits
  10. 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
  11. 15 Apr, 2010 8 commits
  12. 14 Apr, 2010 2 commits
  13. 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