Commits · 7983e339de51f333d885dc1676b0bc64500625f4 · R3 / legacy / bedtools2

Jun 23, 2011
- 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
- Added BamTools object cleanup to the Makefile. · d59bc405
  Aaron authored 13 years ago
  
  d59bc405
- 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
- bamtools GetEndPosition() now defaults to unpadded, zero-based · 4fcfbc85
  Aaron authored 13 years ago
  
  4fcfbc85
- Set BAM compression mode before opening · a446d2fb
  Aaron authored 13 years ago
  
  a446d2fb
- removed multiBamCov from main Makefile · ba585205
  Aaron authored 13 years ago
  
  ba585205
- intersect, window, and gcB support for bamtools1.0 · 9d651d34
  Aaron authored 13 years ago
  
  9d651d34
- coverageBed links with bamtools1.0 · 48c39f82
  Aaron authored 13 years ago
  
  48c39f82
- bedToBam links with bamtools1.0 · aa30e868
  Aaron authored 13 years ago
  
  aa30e868
- preliminary support for bamtools1.0 for bamToBed. · 02f2ab59
  Aaron authored 13 years ago
  
  02f2ab59
- New BamTools 1.0 project structure and Makefile · 92927729
  Aaron authored 13 years ago
  
  92927729
- Added BamTools-Ancillary files · 4b5850cf
  Aaron authored 13 years ago
  
  4b5850cf
Jun 16, 2011
- Changed newline to tab in bamToBed for -tag -bed12. · c9231a25
  Aaron authored 13 years ago
  
  c9231a25
- Further tweak to UCSC mysql help. · 363bce89
  Aaron authored 13 years ago
  
  363bce89
- Fixed multi-line UCSC mysql query in the help for multiple tool. Thanks to Brent Pedersen\! · 25fef4e9
  Aaron authored 13 years ago
  
  25fef4e9
- Patched Assaf Gordon's tweaks to gCB. · 3a7d80fc
  Aaron authored 13 years ago
  
  3a7d80fc
Jun 15, 2011
- Tweaked header in nucBed · 9a83e3d3
  Aaron authored 13 years ago
  
  9a83e3d3
- header and custom pattern search for nucBed. Thanks to Can Alkan. · e7dec439
  Aaron authored 13 years ago
  
  e7dec439
Jun 14, 2011
- Added output description to nucBed help · b6ae6f5e
  Aaron authored 13 years ago
  
  b6ae6f5e
- Improvements to closestBed. Thanks to suggestions by Brent Pedersen, Ryan... · de52bca7
  Aaron authored 13 years ago
  
  Improvements to closestBed. Thanks to suggestions by Brent Pedersen, Ryan Layer, Assaf Gordon, Dan Webster. 1. All overlapping features are reported by closestBed -t all. 2. The "-io" option will prevent overlapping features from being reported.
  de52bca7
- mergeBed now _always_ reports in BED format (i.e., zero-based starts), regardless of input type. · da54ba34
  Aaron authored 13 years ago
  
  da54ba34
- Added -5, -3, -trackline, -trackopts, and -dz options to genomeCoverageBed.... · 5bdfaec0
  Aaron authored 13 years ago
  
  Added -5, -3, -trackline, -trackopts, and -dz options to genomeCoverageBed. Many thanks to Assaf Gordon.
  5bdfaec0
Apr 15, 2011
- First cut at nucBed - profiles DNA sequences defined by BED intervals. · ba39b2e6
  Aaron authored 14 years ago
  
  ba39b2e6
Apr 14, 2011
- Tweaked Makefile and added notboth option to pairToPair. · 9628eca3
  Aaron authored 14 years ago
  
  9628eca3
Apr 08, 2011
- fastaFromBed warns of exceeding length of chromosome and of zero length features. · 82617370
  Aaron authored 14 years ago
  
  82617370
Apr 04, 2011
- Updated version and RELEASE_HISTORY for 2.12.0 · d476534c
  Aaron authored 14 years ago
  
  d476534c
- Improved clarity for zero length features in coverageBed. · be141f5d
  Aaron authored 14 years ago
  
  be141f5d
Apr 01, 2011
- Defaults to other constructors. · 14e45c5c
  Aaron authored 14 years ago
  
  14e45c5c
- Defaults for BED constructors. Cheers to John Marshall for the catch. · d16e39d7
  Aaron authored 14 years ago
  
  d16e39d7
Mar 29, 2011
- logical, not operator. need coffee. · e724885b
  Aaron authored 14 years ago
  
  e724885b
- Fixed overlflow error in pairToPair · 7ded18df
  Aaron authored 14 years ago
  
  7ded18df