Commits · 5d62d8f6d41bccac77a549bed83ec8deaa3762ac · R3 / legacy / bedtools2

Aug 16, 2010
- 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
- Added newline to end of BamAncillary.h · 3cb93de6
  Aaron authored 14 years ago
  
  3cb93de6
- Added newline to end of BamAncillary.cpp to avoid compile warnings. · 46025216
  Aaron authored 14 years ago
  
  46025216
- Added slop to filename when using -slop in bedToIgv. · 7ae8a4d4
  Aaron authored 14 years ago
  
  7ae8a4d4
Jul 04, 2010

Fixed bug in groupBy and added logic to enforce that strings are numeric when... · 7f11baac
Aaron authored 14 years ago
```
Fixed bug in groupBy and added logic to enforce that strings are numeric when asking for nueric ops.
```
7f11baac

Aaron authored 14 years ago

	A. Fixed massive bug in parseBedLine that disallowed BED features with start = 0.  Bad news.
	1. Moved ToString to lineFileUtilities
	2. Added tabFile class.  Works with gzip as well.
	3. Changed groupBy to use the new TabFile class.
	4. Added new collapse feature to groupBy.

3cba5c6c

Fixed string references for strand (i.e. '+' to "+") in windowBed and pairToBed. · e200d064
Aaron authored 14 years ago

e200d064