1. 29 Jan, 2012 1 commit
  2. 13 Jan, 2012 1 commit
  3. 08 Jan, 2012 1 commit
  4. 08 Dec, 2011 2 commits
  5. 09 Nov, 2011 1 commit
  6. 26 Oct, 2011 1 commit
  7. 24 Oct, 2011 1 commit
  8. 28 Sep, 2011 1 commit
  9. 22 Sep, 2011 1 commit
  10. 16 Sep, 2011 4 commits
  11. 31 Aug, 2011 1 commit
  12. 17 Jun, 2011 4 commits
  13. 22 Mar, 2011 1 commit
  14. 02 Feb, 2011 1 commit
  15. 03 Jan, 2011 1 commit
  16. 22 Sep, 2010 1 commit
  17. 21 Sep, 2010 1 commit
  18. 18 Aug, 2010 1 commit
    • Aaron's avatar
      Big commit. · b9ab28d0
      Aaron authored
      	1. Added new version of BamTools supporting uncompressed BAM.
      	2. Added -ubam option to intersectBed.
      	3. First functional release of annotateBed.
      	4. Updated GetEditDistance calls to GetTag(NM) per the new API change in BamTools.
      b9ab28d0
  19. 18 Jul, 2010 2 commits
  20. 17 Jul, 2010 1 commit
  21. 15 Jul, 2010 1 commit
  22. 04 Jul, 2010 1 commit
    • Aaron's avatar
      Fixed logic relating to "split" coverage. · 9fe56c08
      Aaron authored
      	1. Fixed bug in BamAncillary::getBamBlocks where the switch statement was misbehaving.  Changed to if/else
      	2. Added countSplitHits to bedFile class to proper count coverage from "blocked" alignments. Previously, coverage
                 was counted separately for __each__ block yet what we actually want is the base coverage to be counted for each block,
                 but we only want the blocks to be treated as __one__ alignment or feature.
      	3. Updated coverageBed to use getBamBlocks.
      9fe56c08
  23. 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
  24. 29 Jun, 2010 2 commits
  25. 07 Jun, 2010 1 commit
    • 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
  26. 26 Apr, 2010 2 commits
  27. 22 Apr, 2010 1 commit
    • 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
  28. 15 Apr, 2010 3 commits