Commits · ebbbd305c79a4d5126e0e955737807388c274e75 · R3 / legacy / bedtools2

Jan 06, 2011
- Revising README to README.rst · ebbbd305
  Aaron authored 14 years ago
  
  ebbbd305
- Minor formatting in slopBed.cpp. · 3c6c80d8
  Aaron authored 14 years ago
  
  3c6c80d8
- Allowed 8 or 9 column GFF/GTF files. Many thanks to Michael Hoffman. · 6078f7bb
  Aaron authored 14 years ago
  
  6078f7bb
Jan 05, 2011
- Fixed casting issue in windowBed.AddWindow() that cuased slop positions to run... · 4c8e1221
  Aaron authored 14 years ago
  
  Fixed casting issue in windowBed.AddWindow() that cuased slop positions to run off the end of the chromosome.
  4c8e1221
Jan 03, 2011
- Changed BamAlignmentSupportData from private to public. · e2bcd09a
  Aaron authored 14 years ago
  
  This will eliminate the oft-reported compilation issue.
  e2bcd09a
- Added bedGraphFile's Makefile. · f4b3e3af
  Aaron authored 14 years ago
  
  f4b3e3af
- Tabs in Makefile. · 71827777
  Aaron authored 14 years ago
  
  71827777
- Tweaked Makefile. · df14b280
  Aaron authored 14 years ago
  
  df14b280
- Updated Makefile to auto-create obj/ and bin/. · 76fb2a0e
  Aaron authored 14 years ago
  
  76fb2a0e
- Prettied up the code before pushing to github. · b6c80bbc
  Aaron authored 14 years ago
  
  b6c80bbc
Dec 03, 2010
- Updated version to 2.10.2 · 537dd5fa
  Aaron authored 14 years ago
  
  537dd5fa
- Merge branch 'pairToPair_update' · ba7b57f2
  Aaron authored 14 years ago
  
  ba7b57f2
- Fixed pairToPair to allow full "B" entries to be reported in every mode. · b7c0e343
  Aaron authored 14 years ago
  
  b7c0e343
- Tweaked hep for bamToBed · 246d1d8e
  Aaron authored 14 years ago
  
  246d1d8e
Nov 01, 2010
- Added the -cigar option to bamToBed. · 32793b98
  Aaron authored 14 years ago
  
  32793b98
Oct 04, 2010
- Removed careless debugging message from annotateBed. · f81132dc
  Aaron authored 14 years ago
  
  f81132dc
Sep 22, 2010
- Updated Makefile · 0d65d586
  Aaron authored 14 years ago
  
  0d65d586
- Updated release history to reflect 2.10.0 · ffa4389c
  Aaron authored 14 years ago
  
  ffa4389c
- Updated version to 2.10.0 · a543bcef
  Aaron authored 14 years ago
  
  a543bcef
- Update GPL license in source banners. · d9bb1d60
  Aaron authored 14 years ago
  
  d9bb1d60
- Fixed initialization bug in annotateBed constructor. · ba3861a6
  Aaron authored 14 years ago
  
  ba3861a6
Sep 21, 2010
- Added -ubam to pairToBed. · 928dd85b
  Aaron authored 14 years ago
  
  928dd85b
- windowBed supports -ubam. · bd91cd68
  Aaron authored 14 years ago
  
  bd91cd68
- Added -ubam support to intersectBed and bedToBam. · 1cfd5315
  Aaron authored 14 years ago
  
  1cfd5315
- annotateBed can report counts and pct coverage for each annotation file. · 8c37692f
  Aaron authored 14 years ago
  
  8c37692f
- Changed precision for groupBy. · c2664a63
  Aaron authored 14 years ago
  
  c2664a63
- sortBed assumes stdin. · a88aa54d
  Aaron authored 14 years ago
  
  a88aa54d
- slopBed assumes stdin. · 37b4a659
  Aaron authored 14 years ago
  
  37b4a659
- shuffleBed assumes stdin. · 8066526a
  Aaron authored 14 years ago
  
  8066526a
- overlap assumes stdin. · 86d7767e
  Aaron authored 14 years ago
  
  86d7767e
- mergeBed assumes stdin. · d7adcb03
  Aaron authored 14 years ago
  
  d7adcb03
- linksBed assumes stdin. · 0ef7e18a
  Aaron authored 14 years ago
  
  0ef7e18a
- complementBed assumes stdin. · cbeca9e3
  Aaron authored 14 years ago
  
  cbeca9e3
- bedToIgv assumes stdin. · 6074ebc1
  Aaron authored 14 years ago
  
  6074ebc1
- bedToBam assumes stdin. · daf5815d
  Aaron authored 14 years ago
  
  daf5815d
- bed12ToBed6 assumes stdin. · c087a521
  Aaron authored 14 years ago
  
  c087a521
- bamToBed assumes stdin. · 96631891
  Aaron authored 14 years ago
  
  96631891
- GroupBy defaults to stdin and uses -g -c -o as well. · 141a5bf6
  Aaron authored 14 years ago
  
  141a5bf6
- Updated BED struct for future fjoin alg. support. · 3cb18f38
  Aaron authored 14 years ago
  
  3cb18f38
Sep 03, 2010

Aaron authored 14 years ago

	1. Assumes stdin when no -i is given.  Credit = Assaf Gordon
	2. New freqasc and freqdesc options.
	3. Better command line parsing.  Credit = Assaf Gordon.

3112d332