1. 18 Jul, 2010 2 commits
  2. 17 Jul, 2010 6 commits
  3. 15 Jul, 2010 3 commits
  4. 06 Jul, 2010 6 commits
  5. 05 Jul, 2010 4 commits
  6. 04 Jul, 2010 4 commits
    • Aaron's avatar
      Fixed bug in groupBy and added logic to enforce that strings are numeric when... · 7f11baac
      Aaron authored
      Fixed bug in groupBy and added logic to enforce that strings are numeric when asking for nueric ops.
      7f11baac
    • Aaron's avatar
      Large commit. · 3cba5c6c
      Aaron authored
      	A. Fixed massive bug in parseBedLine that disallowed BED features with start = 0.  Bad news.
      	1. Moved ToString to lineFileUtilities
      	2. Added tabFile class.  Works with gzip as well.
      	3. Changed groupBy to use the new TabFile class.
      	4. Added new collapse feature to groupBy.
      3cba5c6c
    • Aaron's avatar
    • 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
  7. 01 Jul, 2010 2 commits
  8. 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
  9. 29 Jun, 2010 4 commits
  10. 08 Jun, 2010 1 commit
  11. 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
  12. 06 May, 2010 2 commits
  13. 05 May, 2010 3 commits