Commits · e186bcbfa9081640eb8feaabb4cd89c0db6be248 · R3 / legacy / bedtools2

Jan 28, 2010
- Version 2.5.0 · e186bcbf
  Aaron authored 15 years ago
  
  e186bcbf
- Added BED+ support and improved GFF/BED distinction. · 1b5fa6d3
  Aaron authored 15 years ago
  
  1b5fa6d3
- Fixed command line bug in bamToBed. · a0250c31
  Aaron authored 15 years ago
  
  a0250c31
- Fixed bug in pairToBed and removed tr1 include. · 53543584
  Aaron authored 15 years ago
  
  1. pairToBed had a bug in the way it parsed -a 2. extraneous tr1/unordered_map include in bedfile.h causes compile issues on some machines.
  53543584
Jan 23, 2010
- Added manual. · 4d85d7cb
  Aaron authored 15 years ago
  
  4d85d7cb
- Updated version to 2.4.2 · b6410bc1
  Aaron authored 15 years ago
  
  b6410bc1
- Corrected commnad line parsing for all tools. · 4f81e90d
  Aaron authored 15 years ago
  
  There was a problem with the way args with a value were being parsed.
  4f81e90d
Jan 19, 2010
- Fixed bug in mergeBed that caused segfault when -nms and -s used together. · 906f5f9e
  Aaron authored 15 years ago
  
  906f5f9e
Jan 11, 2010
- Updated manual. · dc7d63c8
  Aaron authored 15 years ago
  
  dc7d63c8
- Added Derek's changes to BamTools that were causing compile errors. · ab96a16b
  Aaron authored 15 years ago
  
  ab96a16b
- Removed extraneous genome file. · 5dc94065
  Aaron authored 15 years ago
  
  5dc94065
- Removed extraneous data file from src/bamToBed. · d0c84764
  Aaron authored 15 years ago
  
  d0c84764
- Added files to /data · 3b4e5414
  Aaron authored 15 years ago
  
  3b4e5414
- Added /data. · c8142032
  Aaron authored 15 years ago
  
  c8142032
- Cleaned up files from master. · 894bb04a
  Aaron authored 15 years ago
  
  894bb04a
Jan 10, 2010
- Updated HISTORY. · b13487e8
  Aaron authored 15 years ago
  
  b13487e8
- Added BEDTools manual to distribution. · 9998b6f4
  Aaron authored 15 years ago
  
  9998b6f4
- Added example files to /data. · 1f8c8afe
  Aaron authored 15 years ago
  
  1f8c8afe
- Fixed intersectBed Makefile and changed README. · 25ad8693
  Aaron authored 15 years ago
  
  25ad8693
- Cleanup after testing. · f61d87b7
  Aaron authored 15 years ago
  
  f61d87b7
Jan 08, 2010
- Fixed tar goof. · d0e44320
  Aaron authored 15 years ago
  
  d0e44320
- Fixed -type notboth in pairToBed when using -bedpe. · 48427e86
  Aaron authored 15 years ago
  
  48427e86
- Fixes to fastaFromBed maskFastaFromBed · 0c7d1520
  Aaron authored 15 years ago
  
  1. Fixed bugs in parsing command line booleans in fastaFromBed and maskFastaFromBed 2. Added tabular output to fastaFromBed
  0c7d1520
- Added check to fastaFromBed preventing sequences from being · a6e64f5d
  Aaron authored 15 years ago
  
  extract beyond the length of a chromosome.
  a6e64f5d
Jan 07, 2010
- Added support to BEDPE to allow optional fields at the end. · b8fcde3a
  Aaron authored 15 years ago
  
  b8fcde3a
- Updated BEDPE reporting strategy for BAM files. · 19c4838c
  Aaron authored 15 years ago
  
  1. If intrachromosomal, choose the leftmost end. 2. Else, choose the first mate.
  19c4838c
Jan 06, 2010
- Added sanity check to pairToBed · 84fa3f3f
  Aaron authored 15 years ago
  
  84fa3f3f
Jan 05, 2010
- Added -outbam check to intersectBed · 26dc6dda
  Aaron authored 15 years ago
  
  26dc6dda
- Removed -m64 from Makefiles. · 19f7c726
  Aaron authored 15 years ago
  
  19f7c726
- Added mate to name and mapqual as score in intersectBed. · ff4db941
  Aaron authored 15 years ago
  
  - also added map quality as score in pairToBed
  ff4db941
- Fixed bug in mergeBed causing names to be reported twice · dc45a9ab
  Aaron authored 15 years ago
  
  dc45a9ab
- Added +1 to start reporting for GFF features. · 338bc1fd
  Aaron authored 15 years ago
  
  338bc1fd
- Fixed bug in complementBed vis-a-vis Galaxy. · 204128fd
  Aaron authored 15 years ago
  
  204128fd
Jan 04, 2010
- Further standardization of the option listings. · fb5efebf
  Aaron authored 15 years ago
  
  fb5efebf
- Command line option formatting standardized. · 5d29b3c0
  Aaron authored 15 years ago
  
  5d29b3c0
- Cleaned up bedFile.h and added -m64 to Makefiles · 361bf23b
  Aaron authored 15 years ago
  
  361bf23b
- Updated pairToPair. · ca0b7e3b
  Aaron authored 15 years ago
  
  ca0b7e3b
- Imporved BAM support in pairToBed · eaf41f2f
  Aaron authored 15 years ago
  
  eaf41f2f
- Initial BAM support for pairToBed · f908c220
  Aaron authored 15 years ago
  
  f908c220
- Added bamToBed. · e096eb0b
  Aaron authored 15 years ago
  
  e096eb0b