Commits · d4448d675902c3faa5ecb785992ce760b46b4efe · R3 / legacy / bedtools2

Jun 17, 2011
- 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 13 years ago
  
  ba39b2e6
Apr 14, 2011
- Tweaked Makefile and added notboth option to pairToPair. · 9628eca3
  Aaron authored 13 years ago
  
  9628eca3
Apr 08, 2011
- fastaFromBed warns of exceeding length of chromosome and of zero length features. · 82617370
  Aaron authored 13 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
Mar 22, 2011
- Unmapped BAM alignments are now captured by -v in intersectBed and windowBed.... · f2209cfc
  Aaron authored 14 years ago
  
  Unmapped BAM alignments are now captured by -v in intersectBed and windowBed. Thanks to Davide Cittaro.
  f2209cfc
Mar 18, 2011
- Removed Eclipse files. · 83ee0a43
  Aaron authored 14 years ago
  
  83ee0a43
- Corrected stranded logic for + features in flankBed. · 5e0b1650
  Aaron authored 14 years ago
  
  5e0b1650
- Updated flankBed help · 76cc34c7
  Aaron authored 14 years ago
  
  76cc34c7
- Added new flankBed tool. · 95f488dc
  Aaron authored 14 years ago
  
  95f488dc
Mar 11, 2011
- Tweaked an error message in genomeCoverageBed. · f6975ca4
  Aaron authored 14 years ago
  
  f6975ca4
Mar 03, 2011
- Fixed bug in closestBed when B feature's end equal to A feature's start. · 96e3b955
  Aaron authored 14 years ago
  
  96e3b955
- Optionally set masking character (-mc) in maskFastaFromBed. Thanks to Can Alkan. · 96e2ac60
  Aaron authored 14 years ago
  
  96e2ac60
- Made bedToIgv filenames Windows friendly. Thanks to Jiam Wang · 42548a08
  Aaron authored 14 years ago
  
  42548a08