1. 04 Jul, 2010 3 commits
    • 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
  2. 01 Jul, 2010 2 commits
  3. 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
  4. 29 Jun, 2010 4 commits
  5. 08 Jun, 2010 1 commit
  6. 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
  7. 06 May, 2010 2 commits
  8. 05 May, 2010 5 commits
  9. 04 May, 2010 3 commits
  10. 03 May, 2010 2 commits
  11. 29 Apr, 2010 4 commits
  12. 26 Apr, 2010 6 commits
  13. 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
  14. 15 Apr, 2010 3 commits