1. 05 May, 2009 1 commit
    • Aaron Quinlan's avatar
      Strandedness. reportBed in bedFile. peIntersect · ac52b452
      Aaron Quinlan authored
      	1. Added strandedness to relevant programs (e.g. intersectBed, mergeBed, etc.)
      	2. Moved reportBed and reportBedRange to bedFile.cpp to clean up code
      	3. Sped up file parsing.  Added lineFileUtilities.cpp
      	4. Added peIntersectBed
      ac52b452
  2. 29 Apr, 2009 1 commit
  3. 28 Apr, 2009 9 commits
  4. 27 Apr, 2009 1 commit
    • Aaron Quinlan's avatar
      Version 1.2. Added closestBed, linksBed and subtractBed · a1af7c6a
      Aaron Quinlan authored
      	1.  Added subtractBed.
      		A. Fixed bug that prevented "split" overlaps from being reported.
      		B. Prevented A from being reported if >=1 feature in B completely spans it.
      	2.  Added linksBed.
      	3.  Added the ability to define separate windows for upstream and downstream to windowBed.
      a1af7c6a
  5. 26 Apr, 2009 11 commits
  6. 24 Apr, 2009 5 commits
  7. 23 Apr, 2009 6 commits
  8. 21 Apr, 2009 3 commits
    • Aaron Quinlan's avatar
      Changed usage statements to include infor on stdin · 2a308f7b
      Aaron Quinlan authored
      	1. Changed intersectMain.cpp, complementMain.cpp and mergeMain.cpp to
      	   include information on how to run using stdin.
      2a308f7b
    • Aaron Quinlan's avatar
      Updated bedFile.cpp for better stdin support · b89e8b56
      Aaron Quinlan authored
      	1.  Changed BedFile::loadBedFileIntoMapNoBin() to allow either "" or "stdin".
      	2.  Consequently, this allows mergeBed to accept stdin as well.
      b89e8b56
    • Aaron Quinlan's avatar
      Updated mergeBed reporting logic · 80f29d23
      Aaron Quinlan authored
      	1.  Changed the cout statements for the last entries for a chromosome.
      	2.  I had forgotten to report the number of merged entries when -n is requested.
      	3.  I also fixed a bug that occassionally caused the last entry for a chromosome
      	    to report the chrom twice in the output.
      80f29d23
  9. 15 Apr, 2009 2 commits
  10. 10 Apr, 2009 1 commit