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    • Aaron's avatar
      Large update to groupBy. · 3112d332
      Aaron authored 
      	1. Assumes stdin when no -i is given.  Credit = Assaf Gordon
	2. New freqasc and freqdesc options.
	3. Better command line parsing.  Credit = Assaf Gordon.
      3112d332
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  57. 04 Jul, 2010 2 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
  59. 01 Jul, 2010 1 commit
  61. 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