1. 01 Jul, 2010 2 commits
  2. 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
  3. 29 Jun, 2010 4 commits
  4. 08 Jun, 2010 1 commit
  5. 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
  6. 06 May, 2010 2 commits
  7. 05 May, 2010 5 commits
  8. 04 May, 2010 3 commits
  9. 03 May, 2010 2 commits
  10. 29 Apr, 2010 4 commits
  11. 26 Apr, 2010 6 commits
  12. 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
  13. 15 Apr, 2010 6 commits