Commits · 5f125633b8be6f233dac72f54d21986fae0a741b · R3 / legacy / bedtools2

Sep 28, 2011
- -bed now behaves when using bam input in intersectBed. · 5f125633
  Aaron authored 13 years ago
  
  5f125633
Sep 23, 2011
- Release 2.13.2 · 5794cae0
  Aaron authored 13 years ago
  
  5794cae0
- Improved detection of faulty GFF features. · c3f206b5
  Aaron authored 13 years ago
  
  c3f206b5
- Fixed mouse.mm9.genome. Thanks to Charles Plessy. · 420b66ab
  Aaron authored 13 years ago
  
  420b66ab
Sep 22, 2011
- Fixed major bug in intersectBed -split. Thanks to Sol Katzman. · e818f468
  Aaron authored 13 years ago
  
  e818f468
Sep 16, 2011
- removed unused attributes in chromsweep · 2e3c8f96
  Aaron authored 13 years ago
  
  2e3c8f96
- Reworked the nullBed logic. · 6b08d4b5
  Aaron authored 13 years ago
  
  6b08d4b5
- clean up chromsweep interface · c8cd5158
  Aaron authored 13 years ago
  
  c8cd5158
- Moved nullBed reset to GetNextBed · f7b297ff
  Aaron authored 13 years ago
  
  f7b297ff
- Updated README · 28a92d12
  Aaron authored 13 years ago
  
  28a92d12
- Updated README · 5a79210e
  Aaron authored 13 years ago
  
  5a79210e
- Updated README · e0d96029
  Aaron authored 13 years ago
  
  e0d96029
- Updated README · 4bcb6fb5
  Aaron authored 13 years ago
  
  4bcb6fb5
- Added newline before version.h EOF · 7889a020
  Aaron authored 13 years ago
  
  7889a020
- Added new -sorted option to intersectBed. No memory and filthy fast. · 4f951770
  Aaron authored 13 years ago
  
  4f951770
- Gussy. · 0eb0f045
  Aaron authored 13 years ago
  
  0eb0f045
- chromsweep is a proper tool. Now to make it an iterable class. · 5f480366
  Aaron authored 13 years ago
  
  5f480366
- chromsweep is now a python-style generator. Big smile\! · 4f6253a0
  Aaron authored 13 years ago
  
  4f6253a0
Sep 15, 2011
- chromsweep demo · b4928906
  Aaron authored 13 years ago
  
  b4928906
- gcB no longer requires a genome file for BAM. New chromsweep tool. · 2db206ca
  Aaron authored 13 years ago
  
  2db206ca
Sep 14, 2011
- Changed error message when BAM is not qeury sorted in pairToBed · 8a63b8d7
  Aaron authored 13 years ago
  
  8a63b8d7
Sep 11, 2011
- Added Seek and Rewind (destroy?) to BedFile. · 2de3d386
  Aaron authored 13 years ago
  
  2de3d386
Sep 09, 2011
- Added -scores option to tagBam · 0cca2731
  Aaron authored 13 years ago
  
  0cca2731
Sep 07, 2011
- Fixed pairToPair's -type notBoth mode · 47771289
  Aaron authored 13 years ago
  
  47771289
- Version 2.13.1: Added -s, -S, and -names to tagBam. · 403773ce
  Aaron authored 13 years ago
  
  403773ce
Sep 05, 2011
- Added -s, -S, and -names to tagBam. · f2433c5c
  Aaron authored 13 years ago
  
  f2433c5c
Sep 01, 2011
- Avoid deleting bedStream iff stdin · 9b61515e
  Aaron authored 13 years ago
  
  9b61515e
- Reasoning for GZIP detection change. · 557f1afe
  Aaron authored 13 years ago
  
  557f1afe
- Proper Gzip check · 48d2065e
  Aaron authored 13 years ago
  
  48d2065e
- Updated gzip detection. Weaker, but necessary for FIFO support · ec2ec9b2
  Aaron authored 13 years ago
  
  ec2ec9b2
- Gzip detected by file extension. Weak, but only approach that works at this point. · 12fc63b3
  Aaron authored 13 years ago
  
  12fc63b3
- Need to rewind to start of file after Gzip check. · d6548970
  Aaron authored 13 years ago
  
  d6548970
- Updated fastaFromBed · 4a87714b
  Aaron authored 13 years ago
  
  4a87714b
- fifo support add'l · c6393533
  Aaron authored 13 years ago
  
  c6393533
Aug 31, 2011
- Reverted the -full option in fastaFromBed. Use 06a7e24e294e06258c75 to retain it. · 8311a2cf
  Aaron authored 13 years ago
  
  8311a2cf
- BEDTools now supports FIFOs and named pipes. Many thanks Nate Weeks and... · f7990341
  Aaron authored 13 years ago
  
  BEDTools now supports FIFOs and named pipes. Many thanks Nate Weeks and Michael Hoffman for the suggestions.
  f7990341
- now allow "-" as well as "stdin". · c1811a8a
  Aaron authored 13 years ago
  
  c1811a8a
- Added -Sm to windowBed · adf85fd4
  Aaron authored 13 years ago
  
  adf85fd4
- Added -S to subtractBed · 39ce5531
  Aaron authored 13 years ago
  
  39ce5531
- Added -S to pairToBed · 793ec9f3
  Aaron authored 13 years ago
  
  793ec9f3