Commits · 90af6a76f05c28bfd3a5e81a77a1a50eddebea9a · R3 / legacy / bedtools2

Dec 22, 2014
- allow closest ties that don't overlap. · 90af6a76
  arq5x authored 10 years ago
  
  90af6a76
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
Nov 05, 2014
- Corrections and unit tests for closest -D option. · 5d20ecfd
  Neil Kindlon authored 10 years ago
  
  5d20ecfd
Nov 03, 2014
- Bug fixes and more unit tests for closest · 8a2e3695
  Neil Kindlon authored 10 years ago
  
  8a2e3695
Nov 01, 2014
- first check-in for new closest tool · 897d1a85
  Neil Kindlon authored 10 years ago
  
  897d1a85
Oct 27, 2014

fix bamToFastq skipping reads after unpaired reads · 41f96cf0

Ryan Williams authored 10 years ago

It was correctly identifying reads whose “paired” flag was set, but then
it was incorrectly skipping over the read-pair that follows such an
incorrect read.

Also added a test for this behavior.

41f96cf0

Sep 18, 2014
- Stop Chromsweeep cache scan when DB is after query; allow BAM unmapped reads/chrom in genome file. · 7434d8a3
  nkindlon authored 10 years ago
  
  7434d8a3
Aug 15, 2014
- Changes for multi-DB intersection. · 56761cd4
  nkindlon authored 10 years ago
  
  56761cd4
Jul 24, 2014
- make sure it doesn't accumulate · b22d89e6
  Brent Pedersen authored 10 years ago
  
  b22d89e6
- fix slop with -pct · ecb4afaa
  Brent Pedersen authored 10 years ago
  
  ecb4afaa
Jul 07, 2014
- Corrected errors caused during merge-conflict resolution · 57ed945c
  nkindlon authored 10 years ago
  
  57ed945c
Jul 04, 2014
- Check stderr is empty, not stdout (fixes test for #46) · b84b1823
  John Marshall authored 11 years ago
  
  b84b1823
Jul 02, 2014
- Multiple DB intersect support with unit tests and updated help messages. · 509cc91d
  nkindlon authored 10 years ago
  
  509cc91d
May 29, 2014
- Added new -iobuf option and unit tests. · ccd125c1
  nkindlon authored 10 years ago
  
  ccd125c1
May 23, 2014
- Fixed bug for files with no newlines. · d8c62016
  nkindlon authored 10 years ago
  
  d8c62016
- fix for slop bug in issue \#82 · 4a5fc54a
  arq5x authored 10 years ago
  
  4a5fc54a
May 22, 2014
- correct intersect unit test - was pointing to test binary · 69eb4eaa
  arq5x authored 10 years ago
  
  69eb4eaa
- More unit tests for column ops on BAM · bc90a1a0
  nkindlon authored 10 years ago
  
  bc90a1a0
May 17, 2014
- Changes fetch columns by number from BAM files. · 952140cc
  nkindlon authored 10 years ago
  
  952140cc
May 08, 2014
- Stripped whitespace and DOS endLine chars in parsing. · 2ae5c07a
  nkindlon authored 10 years ago
  
  2ae5c07a
May 06, 2014
- Updated map's unit test for allowance of numeric ops on non-num cols · 47a801b9
  nkindlon authored 10 years ago
  
  47a801b9
- Allowed numeric ops for non-numeric columns · 9ee6bac8
  nkindlon authored 10 years ago
  
  9ee6bac8
Apr 30, 2014
- Added unit test to merge to confirm precision · be32e1c1
  nkindlon authored 10 years ago
  
  be32e1c1
- Added stranded info to jaccard and merge help, fixed stranded jaccard bug · 39fffc97
  nkindlon authored 10 years ago
  
  39fffc97
Apr 25, 2014
- Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug,... · e2be0789
  nkindlon authored 10 years ago
  
  Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug, added unit test in sample.
  e2be0789
Apr 24, 2014
- Made Merge only print Bed3 output for BAM, added unit test · bbda1f41
  nkindlon authored 10 years ago
  
  bbda1f41
- merge bug fixes and unit tests · b740bbf4
  nkindlon authored 10 years ago
  
  b740bbf4
Apr 17, 2014
- cleanup unit tests. · 17ec9aa9
  arq5x authored 10 years ago
  
  17ec9aa9
- Final unit tests for merge, including stranded merge bug fixes. · 1b866b6e
  nkindlon authored 10 years ago
  
  1b866b6e
Apr 16, 2014
- Unit tests and bug fixes for merge release · 5eb3b68c
  nkindlon authored 10 years ago
  
  5eb3b68c
Apr 15, 2014
- Handling empty files with headers · fe5ea0ed
  nkindlon authored 10 years ago
  
  fe5ea0ed