Commits · f12f568c80c3201b84fc16d23ef9b6cd1bd270c4 · R3 / legacy / bedtools2

Aug 31, 2011
- Added -S to closestBed · f12f568c
  Aaron authored 13 years ago
  
  f12f568c
- Added -S to annotateBed · 1348016b
  Aaron authored 13 years ago
  
  1348016b
- Added -S to coverageBed · a3c8e702
  Aaron authored 13 years ago
  
  a3c8e702
- Added -S (opposite strand) logic to intersectBed · 8e72b209
  Aaron authored 13 years ago
  
  8e72b209
- Added logic to keep dups and failed QC for multiBamCov. Thanks to Chip Stewart. · afc844d4
  Aaron authored 13 years ago
  
  afc844d4
Jul 25, 2011
- GFF can't have 0-length features. · 04a6b489
  Aaron authored 13 years ago
  
  04a6b489
Jul 19, 2011
- Added -full to fastaFromBed · 7207d6ea
  Aaron authored 13 years ago
  
  7207d6ea
Jul 13, 2011
- Corrected start check in parseVcfLine. Thanks to Jan Vogel · 7894c168
  Aaron authored 13 years ago
  
  7894c168
Jul 06, 2011
- First cut at -scale for genomeCoverageBed · 7f59389c
  Aaron authored 13 years ago
  
  7f59389c
Jul 05, 2011
- corrected a pull goof · 63129a25
  Aaron authored 13 years ago
  
  63129a25
- included cstdlib in lineFileUtilities.h. Thanks to @daler · 92fb9725
  Aaron authored 13 years ago
  
  92fb9725
- include cstdlib for gcc 4.4.3 · 641666ee
  daler authored 13 years ago
  
  641666ee
Jul 01, 2011
- Tweaks to Tokenize(), GetNextBed(), and detection of negative coordinates. Thanks to @agordon · a3c8e94d
  Aaron authored 13 years ago
  
  a3c8e94d
Jun 30, 2011
- 15% speedup for the tokenizer. · 59d77134
  Aaron authored 13 years ago
  
  59d77134
Jun 29, 2011
- tweak to Fasta.cpp · 45952e64
  Aaron authored 13 years ago
  
  45952e64
- Changed version number · a764f2c7
  Aaron authored 13 years ago
  
  a764f2c7
- Updated help messages · da8bf325
  Aaron authored 13 years ago
  
  da8bf325
- Latest BamTools. Commit 525fc971414d7f7b8b60 · 26f4b896
  Aaron authored 13 years ago
  
  26f4b896
- Don't track BamTools/include · 31708e4a
  Aaron authored 13 years ago
  
  31708e4a
- Cleanup of bamtools directories and updated Make · 80c60e99
  Aaron authored 13 years ago
  
  80c60e99
- New region checks for multiBamCov. Thanks to Derek Barnett. · 3001efad
  Aaron authored 13 years ago
  
  3001efad
Jun 28, 2011
- Updated to 2.13.0.alpha · 48f83463
  Aaron authored 13 years ago
  
  48f83463
Jun 24, 2011
- User can define their own tag type for tagBam. · 9fc914ad
  Aaron authored 13 years ago
  
  9fc914ad
- Moved FastaHack to the utils/ directory · 5490e938
  Aaron authored 13 years ago
  
  5490e938
- Code gussying · bb1b7cca
  Aaron authored 13 years ago
  
  bb1b7cca
Jun 23, 2011
- Updated tagBam help so that it actually works... · aef05843
  Aaron authored 13 years ago
  
  aef05843
- Added -f to tagBam. · 7731f7f3
  Aaron authored 13 years ago
  
  7731f7f3
- Pushed tagBam to GitHub · 0b3f2511
  Aaron authored 13 years ago
  
  0b3f2511
- Added -counts option to coverageBed to only collect the count of overlaps (no pct., etc.) · 86d41f16
  Aaron authored 13 years ago
  
  86d41f16
- multiBamCov tweak · 7983e339
  Aaron authored 13 years ago
  
  7983e339
- Added minQual (-q) and force proper pairs (-p) to multiBamCov. · cc031ba9
  Aaron authored 13 years ago
  
  cc031ba9
Jun 22, 2011
- Clean Bamtools objects · 8825a154
  Aaron authored 13 years ago
  
  8825a154
- Tweaked Makefile and using GetNextAlignment() in multiBamCov. · 743f05bd
  Aaron authored 13 years ago
  
  743f05bd
Jun 17, 2011
- make Bamtools/lib on the fly · 67ae0999
  Aaron authored 13 years ago
  
  67ae0999
- make Bamtools/lib on the fly · 6cd47e25
  Aaron authored 13 years ago
  
  6cd47e25
- aded Bamtools/lib · ee3864c8
  Aaron authored 13 years ago
  
  ee3864c8
- aded Bamtools/lib · c9a2e73a
  Aaron authored 13 years ago
  
  c9a2e73a
- First cut at new multiBamCov tool. I like. · d4448d67
  Aaron authored 13 years ago
  
  d4448d67
- Hooray, support for BamTools 1.0. Many good things to come. · 773e1ae4
  Aaron authored 13 years ago
  
  773e1ae4
- specifically request unpadded and 1-based ends from GetEndCoordinate() · 473c192c
  Aaron authored 13 years ago
  
  473c192c