Commits · 2db206caea5a3ce69a280b33cc65a0e6b1b50b2b · R3 / legacy / bedtools2

Sep 15, 2011
- 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
- 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 11, 2011
- Makefile tweak · 37898378
  Aaron authored 13 years ago
  
  37898378
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
- Merge branch 'master' of github.com:arq5x/bedtools · 2916f0c4
  Aaron authored 13 years ago
  
  2916f0c4
- included cstdlib in lineFileUtilities.h. Thanks to @daler · 92fb9725
  Aaron authored 13 years ago
  
  92fb9725
- Merge pull request #7 from daler/master · e2872ef4
  Aaron Quinlan authored 13 years ago
  
  include <cstdlib> in lineFileUtilities.h for gcc 4.4.3
  e2872ef4
- 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