Commits · c2c287469079d1f6ae95c486c76b4e97a6d59e11 · R3 / legacy / bedtools2

Dec 12, 2011
- First pass at new, consolidated CLI. · c2c28746
  Aaron authored 13 years ago
  
  c2c28746
Dec 08, 2011
- preliminary · 0ef7f2dd
  Aaron authored 13 years ago
  
  0ef7f2dd
- makefile tweak · f98028d5
  Aaron authored 13 years ago
  
  f98028d5
- Comment fix. · 9dda8b7f
  Aaron authored 13 years ago
  
  9dda8b7f
- Further nullBed tweaking. · 5c3d96db
  Aaron authored 13 years ago
  
  5c3d96db
- return true on BLANK · 600a99ca
  Aaron authored 13 years ago
  
  600a99ca
- Removed nullBed nonsense. · 4406c1ef
  Aaron authored 13 years ago
  
  4406c1ef
- bamToBed -bedpe now handles singletons. · b3ba4b98
  Aaron authored 13 years ago
  
  b3ba4b98
- Removed need for nullBed. clear() otherFields in GetNextBed(). · 77dbc361
  Aaron authored 13 years ago
  
  77dbc361
- Added -header to sortBed · e8909692
  Aaron authored 13 years ago
  
  e8909692
- Use new GetNextBed() interface. Redux. · 696f8a89
  Aaron authored 13 years ago
  
  696f8a89
- Use new GetNextBed() interface. · 520ccaae
  Aaron authored 13 years ago
  
  520ccaae
Dec 07, 2011
- rename tool to acvoid conflicts. s/overlap/getOverlap · dfb191ce
  Aaron authored 13 years ago
  
  dfb191ce
- Makefile aborts on first error. · 9821cf1f
  Aaron authored 13 years ago
  
  9821cf1f
Nov 29, 2011
- Add'l comments. · 705c2aaa
  Aaron authored 13 years ago
  
  705c2aaa
- Comments for header logic. · 250d1546
  Aaron authored 13 years ago
  
  250d1546
- force ^chrom ^track and ^browser headers to only occur on the first line. · d8d64134
  Aaron authored 13 years ago
  
  d8d64134
- Allow headers to start with "chrom" · 44775518
  Aaron authored 13 years ago
  
  44775518
- lineNum is now tracked privately. · b4b12ca5
  Aaron authored 13 years ago
  
  b4b12ca5
- Merge branch 'read_write_headers' · 8d6cc8dc
  Aaron authored 13 years ago
  
  8d6cc8dc
- Added unstaged files. · f909a024
  Aaron authored 13 years ago
  
  f909a024
- Added -header to intersect, window, closest, slop, flank. · 32cb6584
  Aaron authored 13 years ago
  
  32cb6584
Nov 25, 2011
- Fiex off-by-one in linksBed. · 5b293cfd
  Aaron authored 13 years ago
  
  5b293cfd
Nov 17, 2011
- Fixed getBamBlocks() · 3491dd54
  Aaron authored 13 years ago
  
  3491dd54
- Added intervals option to tagBam. · f82d2d22
  Aaron authored 13 years ago
  
  f82d2d22
Nov 16, 2011
- Makefile tweak. · a43e8f68
  Aaron authored 13 years ago
  
  a43e8f68
- Added bedpeToBam Makefile · 8d6cb613
  Aaron authored 13 years ago
  
  8d6cb613
- Changes for CSHL course. · a0846e8f
  Aaron authored 13 years ago
  
  a0846e8f
Nov 09, 2011
- Added methods to store and report file headers upon request. · 79c6a2ff
  Aaron authored 13 years ago
  
  79c6a2ff
- minor · 65b0c56b
  Aaron authored 13 years ago
  
  65b0c56b
Nov 08, 2011
- explain the sorting criteria. it's odd thanks to STL PQ behavior. · fef9876e
  Aaron authored 13 years ago
  
  fef9876e
- Merge branch 'cluster' · af90cd9e
  Aaron authored 13 years ago
  
  af90cd9e
- Added r. layer's cluster algorithm -cluster · 025efbd1
  Aaron authored 13 years ago
  
  025efbd1
Nov 07, 2011
- bwa mode · 10e90122
  Aaron authored 13 years ago
  
  10e90122
- bwa mode · fae3a320
  Aaron authored 13 years ago
  
  fae3a320
Nov 04, 2011
- -novo option in bamToBed · 4667a7ab
  Aaron authored 13 years ago
  
  4667a7ab
Nov 03, 2011
- No need to force chroms to be sorted. Avoid diff.s b/w chr1 and 1 · b0548654
  Aaron authored 13 years ago
  
  b0548654
- Updated banner and help for multiIntersectBed. · 054fc857
  Aaron authored 13 years ago
  
  054fc857
- Handle header lines for new version of GetNextBed · 341b4d42
  Aaron authored 13 years ago
  
  341b4d42
- Updated version. · 32e9e7b2
  Aaron authored 13 years ago
  
  32e9e7b2