Commits · 567477f3f4acdfbf6b131491ab090fbc517d0c28 · R3 / legacy / bedtools2

Apr 23, 2015
- Fixed bug 223, Insertions for VCF records. Added unit test. · 567477f3
  Neil Kindlon authored 9 years ago
  
  567477f3
Feb 26, 2015
- added unit tests for -sorted and multiple databases. · 706608e5
  Neil Kindlon authored 10 years ago
  
  706608e5
- First check-in for new version of subtract · 6961cd20
  Neil Kindlon authored 10 years ago
  
  6961cd20
Feb 23, 2015
- Added unit test for closest to check -header option · 4abcc2b0
  Neil Kindlon authored 10 years ago
  
  4abcc2b0
- Fixed bug for -nonamecheck, added help, unit test · 78c266dc
  Neil Kindlon authored 10 years ago
  
  78c266dc
Feb 21, 2015
- all tests pass · efda13cb
  jayhesselberth authored 10 years ago
  
  efda13cb
- test stubs; ``-n`` is excepting now · 66b1d64f
  jayhesselberth authored 10 years ago
  
  66b1d64f
- test stub; refactor num_window calculation · d98c7f8f
  jayhesselberth authored 10 years ago
  
  d98c7f8f
Feb 14, 2015
- forgot new test files for intersect unit tests · 4a9a6c2b
  Neil Kindlon authored 10 years ago
  
  4a9a6c2b
Feb 13, 2015
- bug fixes for kclosest sorted output, 0 length records, and map a vs b file with multi-dbs · dbc19ad2
  Neil Kindlon authored 10 years ago
  
  dbc19ad2
Jan 26, 2015
- yet another merge error · e7656ff4
  Neil Kindlon authored 10 years ago
  
  e7656ff4
- another merge error · 217cad41
  Neil Kindlon authored 10 years ago
  
  217cad41
- Added files · 90892a6b
  Neil Kindlon authored 10 years ago
  
  90892a6b
- Added closest -fu and -fd, updated help · 29fe57fc
  Neil Kindlon authored 10 years ago
  
  29fe57fc
- addressing merge conflict · 60f99fb0
  Neil Kindlon authored 10 years ago
  
  60f99fb0
- K closest finally working; chrom name conventions test change · 24e97ccb
  Neil Kindlon authored 10 years ago
  
  24e97ccb
Jan 10, 2015
- simple algorithm when n< FOPEN_MAX · 3398f726
  Pierre Lindenbaum authored 10 years ago
  
  3398f726
Jan 09, 2015
- bedtools split · e53d6086
  lindenb authored 10 years ago
  
  e53d6086
Jan 07, 2015
- Fixed bug167: stranded chromsweep wasn't working · 9d4ed4c7
  Neil Kindlon authored 10 years ago
  
  9d4ed4c7
Dec 23, 2014
- Fixed bug157: ties not prevented by -iu/-id · effc83ef
  Neil Kindlon authored 10 years ago
  
  effc83ef
Dec 22, 2014
- allow closest ties that don't overlap. · 90af6a76
  arq5x authored 10 years ago
  
  90af6a76
Dec 20, 2014
- Removed test debugging files from repository · 26618897
  Neil Kindlon authored 10 years ago
  
  26618897
- Removed large closest tests from repository · e94c559e
  Neil Kindlon authored 10 years ago
  
  e94c559e
- More sort order unit tests for chromsweep and closest; bug fixes and minor enhancements · 4422985d
  Neil Kindlon authored 10 years ago
  
  4422985d
Dec 18, 2014
- Forgot a new test file for closest · 2a2ae0cd
  Neil Kindlon authored 10 years ago
  
  2a2ae0cd
- Bug fixes for closest and bug 155 · 436e6f4e
  Neil Kindlon authored 10 years ago
  
  436e6f4e
Dec 07, 2014
- Added tleonardi's changes for bug 150 re: overlap bases with -split in intersect · b70b6caf
  Neil Kindlon authored 10 years ago
  
  b70b6caf
Dec 06, 2014
- Cleaned up error message for sort order detection of missing chrom · a2cacdf7
  Neil Kindlon authored 10 years ago
  
  a2cacdf7
- Updated jaccard unit test to reflect chromsweep change · b561a2f4
  Neil Kindlon authored 10 years ago
  
  b561a2f4
- Detect differently ordered files in chromsweep and closest. Merged Fisher changes. · 4c7213c5
  Neil Kindlon authored 10 years ago
  
  4c7213c5
Dec 02, 2014

update NewChromSweep signature to support fisher. May have conflicts with... · 6ae90161

arq5x authored 10 years ago

update NewChromSweep signature to support fisher. May have conflicts with @nkindlon's upcoming changes. Will resolve then.

6ae90161

Nov 26, 2014
- tuning, testing and docs for fisher · ed4e8a9a
  Brent Pedersen authored 10 years ago
  
  ed4e8a9a
Nov 25, 2014
- scripts for comparing to shuffled · c3ab3d1e
  Brent Pedersen authored 10 years ago
  
  c3ab3d1e
- change fisher to use numbers of intervals rather than bases of overlap · d6544e0e
  Brent Pedersen authored 10 years ago
  
  d6544e0e
Nov 19, 2014
- added -prec option, default 10. Updated unit tests for merge, map, jaccard.... · 3b5afaf7
  Neil Kindlon authored 10 years ago
  
  added -prec option, default 10. Updated unit tests for merge, map, jaccard. Accept stdin by default in merge.
  3b5afaf7
Nov 18, 2014
- restore defaukt precision in groupby · a60ae746
  arq5x authored 10 years ago
  
  a60ae746
Nov 11, 2014
- VcfRecord code cleanup, add intersect unit test test for VCF SV's. · 858cc4bd
  Neil Kindlon authored 10 years ago
  
  858cc4bd
Nov 10, 2014
- Read VCF struct vars length from SVLEN tag instead of using length of varRef field · 0b8612d3
  Neil Kindlon authored 10 years ago
  
  0b8612d3
- Fixed bug133, missing intersection of zero length records · 0ea1769d
  Neil Kindlon authored 10 years ago
  
  0ea1769d
Nov 07, 2014
- Fixed bug 100, allowing scientific notation for coords, not returning INT_MIN for invalid numbers · 5ba347e1
  Neil Kindlon authored 10 years ago
  
  5ba347e1