Commits · 0d65d58669018ec41df172d97f3bffd46224144b · R3 / legacy / bedtools2

Sep 22, 2010
- Updated Makefile · 0d65d586
  Aaron authored 14 years ago
  
  0d65d586
- Updated release history to reflect 2.10.0 · ffa4389c
  Aaron authored 14 years ago
  
  ffa4389c
- Updated version to 2.10.0 · a543bcef
  Aaron authored 14 years ago
  
  a543bcef
- Update GPL license in source banners. · d9bb1d60
  Aaron authored 14 years ago
  
  d9bb1d60
- Fixed initialization bug in annotateBed constructor. · ba3861a6
  Aaron authored 14 years ago
  
  ba3861a6
Sep 21, 2010
- Added -ubam to pairToBed. · 928dd85b
  Aaron authored 14 years ago
  
  928dd85b
- windowBed supports -ubam. · bd91cd68
  Aaron authored 14 years ago
  
  bd91cd68
- Added -ubam support to intersectBed and bedToBam. · 1cfd5315
  Aaron authored 14 years ago
  
  1cfd5315
- annotateBed can report counts and pct coverage for each annotation file. · 8c37692f
  Aaron authored 14 years ago
  
  8c37692f
- Changed precision for groupBy. · c2664a63
  Aaron authored 14 years ago
  
  c2664a63
- sortBed assumes stdin. · a88aa54d
  Aaron authored 14 years ago
  
  a88aa54d
- slopBed assumes stdin. · 37b4a659
  Aaron authored 14 years ago
  
  37b4a659
- shuffleBed assumes stdin. · 8066526a
  Aaron authored 14 years ago
  
  8066526a
- overlap assumes stdin. · 86d7767e
  Aaron authored 14 years ago
  
  86d7767e
- mergeBed assumes stdin. · d7adcb03
  Aaron authored 14 years ago
  
  d7adcb03
- linksBed assumes stdin. · 0ef7e18a
  Aaron authored 14 years ago
  
  0ef7e18a
- complementBed assumes stdin. · cbeca9e3
  Aaron authored 14 years ago
  
  cbeca9e3
- bedToIgv assumes stdin. · 6074ebc1
  Aaron authored 14 years ago
  
  6074ebc1
- bedToBam assumes stdin. · daf5815d
  Aaron authored 14 years ago
  
  daf5815d
- bed12ToBed6 assumes stdin. · c087a521
  Aaron authored 14 years ago
  
  c087a521
- bamToBed assumes stdin. · 96631891
  Aaron authored 14 years ago
  
  96631891
- GroupBy defaults to stdin and uses -g -c -o as well. · 141a5bf6
  Aaron authored 14 years ago
  
  141a5bf6
- Updated BED struct for future fjoin alg. support. · 3cb18f38
  Aaron authored 14 years ago
  
  3cb18f38
Sep 03, 2010

Aaron authored 14 years ago

	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

Aug 18, 2010

Big commit. · b9ab28d0

Aaron authored 14 years ago

	1. Added new version of BamTools supporting uncompressed BAM.
	2. Added -ubam option to intersectBed.
	3. First functional release of annotateBed.
	4. Updated GetEditDistance calls to GetTag(NM) per the new API change in BamTools.

b9ab28d0

Aug 16, 2010
- Updated groupBy examples. · 8959e80f
  Aaron authored 14 years ago
  
  8959e80f
- Updated the unionBedGraphs help. · 7f8b94ca
  Aaron authored 14 years ago
  
  7f8b94ca
- Updated version. · 74963a20
  Aaron authored 14 years ago
  
  74963a20
- Cleaned up groupBy and unionBedFiles. · 939d5390
  Aaron authored 14 years ago
  
  939d5390
- Improved the error checking for unionBedGraphs. · 2ff5a753
  Aaron authored 14 years ago
  
  2ff5a753
- First commit for unionBedGraphs and multi-column groupBy. · 5d62d8f6
  Aaron authored 14 years ago
  
  5d62d8f6
Aug 06, 2010
- Minor tweaks. · 8925af09
  Aaron authored 14 years ago
  
  8925af09
- Added feature to get distance to closest feature (-d). Thanks to Erik Arner. · 90464038
  Aaron authored 14 years ago
  
  90464038
- Added per base coverage (-d) to coverageBed and cleaned up the main loop. · 7b2ca585
  Aaron authored 14 years ago
  
  7b2ca585
Aug 05, 2010
- Fixed overflow bug in slopBed causing starts and ends beyod the size of the chrom. · 9b2eb4e6
  Aaron authored 14 years ago
  
  9b2eb4e6
Aug 04, 2010
- Changed UINT from 16 bit to 32 bit in bedFile. Resolves issue 21. · 67d54910
  Aaron authored 14 years ago
  
  67d54910
- Fixed bug reporting in either mode for pairToPair. · 7c13f932
  Aaron authored 14 years ago
  
  7c13f932
- Fixed bug preventing closest feature detection for features with start < 2048000. · 0bbd02c3
  Aaron authored 14 years ago
  
  0bbd02c3
- Multiple changes. · 5d8e5739
  Aaron authored 14 years ago
  
  1. Fixed bug where an extra tab is inserted prior to \n in the report*Newline methods. 2. Fixed bug causing incorrect behavior when first bed feature has stant and end = 0.
  5d8e5739
Jul 26, 2010
- Fixed bug in parsing lines that caused some GFF files to be detected as VCF. · 09c74134
  Aaron authored 14 years ago
  
  09c74134