Commits · b9ab28d05ce8051f4631f6469fd2c9578978840c · R3 / legacy / bedtools2

Aug 18, 2010

Big commit. · b9ab28d0

Aaron authored 14 years ago

	1. Added new version of BamTools supporting uncompressed BAM.
	2. Added -ubam option to intersectBed.
	3. First functional release of annotateBed.
	4. Updated GetEditDistance calls to GetTag(NM) per the new API change in BamTools.

b9ab28d0

Aug 16, 2010
- Updated groupBy examples. · 8959e80f
  Aaron authored 14 years ago
  
  8959e80f
- Updated the unionBedGraphs help. · 7f8b94ca
  Aaron authored 14 years ago
  
  7f8b94ca
- Updated version. · 74963a20
  Aaron authored 14 years ago
  
  74963a20
- Cleaned up groupBy and unionBedFiles. · 939d5390
  Aaron authored 14 years ago
  
  939d5390
- Improved the error checking for unionBedGraphs. · 2ff5a753
  Aaron authored 14 years ago
  
  2ff5a753
- First commit for unionBedGraphs and multi-column groupBy. · 5d62d8f6
  Aaron authored 14 years ago
  
  5d62d8f6
Aug 06, 2010
- Minor tweaks. · 8925af09
  Aaron authored 14 years ago
  
  8925af09
- Added feature to get distance to closest feature (-d). Thanks to Erik Arner. · 90464038
  Aaron authored 14 years ago
  
  90464038
- Added per base coverage (-d) to coverageBed and cleaned up the main loop. · 7b2ca585
  Aaron authored 14 years ago
  
  7b2ca585
Aug 05, 2010
- Fixed overflow bug in slopBed causing starts and ends beyod the size of the chrom. · 9b2eb4e6
  Aaron authored 14 years ago
  
  9b2eb4e6
Aug 04, 2010
- Changed UINT from 16 bit to 32 bit in bedFile. Resolves issue 21. · 67d54910
  Aaron authored 14 years ago
  
  67d54910
- Fixed bug reporting in either mode for pairToPair. · 7c13f932
  Aaron authored 14 years ago
  
  7c13f932
- Fixed bug preventing closest feature detection for features with start < 2048000. · 0bbd02c3
  Aaron authored 14 years ago
  
  0bbd02c3
- Multiple changes. · 5d8e5739
  Aaron authored 14 years ago
  
  1. Fixed bug where an extra tab is inserted prior to \n in the report*Newline methods. 2. Fixed bug causing incorrect behavior when first bed feature has stant and end = 0.
  5d8e5739
Jul 26, 2010
- Fixed bug in parsing lines that caused some GFF files to be detected as VCF. · 09c74134
  Aaron authored 14 years ago
  
  09c74134
Jul 23, 2010
- Fixed bug in detecting whether or not columns are numeric. · 31f051d2
  Aaron authored 14 years ago
  
  31f051d2
- Added GetTag logic for bamToBed · 71bb92d8
  Aaron authored 14 years ago
  
  71bb92d8
Jul 22, 2010
- Added <cctype> includes to BamAux.h and sequenceUtilities.h · 15f971f0
  Aaron authored 14 years ago
  
  15f971f0
- Resetting the master from stupid little changes. · e9337301
  Aaron authored 14 years ago
  
  e9337301
Jul 21, 2010
- Undid a stupid change I made to BGZF.cpp · 025b18e9
  Aaron authored 14 years ago
  
  025b18e9
Jul 18, 2010
- Fixed bug in Makefiles calling fileType.o "filetype.o" · f2543820
  Aaron authored 14 years ago
  
  f2543820
- Changes to RELEASE_HISTORY and VERSION and chmods · 7f513c62
  Aaron authored 14 years ago
  
  7f513c62
- Added fileType.cpp to auto-detect gzipped files (Thanks to Assaf Gordon.) · df065ac7
  Aaron authored 14 years ago
  
  Tweaks to processHits in intersectBed for speed.
  df065ac7
Jul 17, 2010
- Updated overlap usage statement. · a4c67773
  Aaron authored 14 years ago
  
  a4c67773
- Fixed bug in FindOneOrMoreOverlapsPerBin. · 5eaca61d
  Aaron authored 14 years ago
  
  The overlap variable was a CHRPOS. The negative overlaps were reported as positive causing false hits when using BAM input.
  5eaca61d
- Defined the name field for VCF files. · 3d59c09c
  Aaron authored 14 years ago
  
  3d59c09c
- Updated the usage statements to reflect bed/gff/vcf support. · a79ec216
  Aaron authored 14 years ago
  
  a79ec216
- Fixed compilation issues with groupBy and bedToIgv. · 5d31229d
  Aaron authored 14 years ago
  
  5d31229d
- Removed omp.h include from bedToBam. · b90e5fb8
  Aaron authored 14 years ago
  
  b90e5fb8
Jul 15, 2010
- Added checks to groupBy to prevent the selection of improper opCols and groups. · da5edfe7
  Aaron authored 14 years ago
  
  da5edfe7
- Fixed bug in intersectBed causing -r to not report the same result when files are swapped. · 39f6414d
  Aaron authored 14 years ago
  
  39f6414d
- Fixed a bug in bedFile.h preventing GFF strands from being read properly. · 1bd3aa03
  Aaron authored 14 years ago
  
  1bd3aa03
Jul 06, 2010
- Tracking the tabFile Makefile. · fb8fbc97
  Aaron authored 14 years ago
  
  fb8fbc97
- Updated the pairToPair usage statement. · d583943d
  Aaron authored 14 years ago
  
  d583943d
- Created an "either" mode for pairToPair. · 45306c09
  Aaron authored 14 years ago
  
  45306c09
- Improved the usage statement for groupBy and bedToIgv. · 74b0da44
  Aaron authored 14 years ago
  
  74b0da44
- Added bedToIgv to the release. · e0cef21a
  Aaron authored 14 years ago
  
  e0cef21a
- Tweaked the includes in tabFile.h and groupBy.cpp · fc089df8
  Aaron authored 14 years ago
  
  fc089df8
Jul 05, 2010
- Updated RELEASE_HISTORY. · 7ba65284
  Aaron authored 14 years ago
  
  7ba65284